I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 11 05:49:46 +14 2020 I: pbuilder-time-stamp: 1591804186 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [biojava4-live_4.2.12+dfsg-2.dsc] I: copying [./biojava4-live_4.2.12+dfsg.orig.tar.xz] I: copying [./biojava4-live_4.2.12+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Jan 19 09:48:29 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biojava4-live_4.2.12+dfsg-2.dsc dpkg-source: info: extracting biojava4-live in biojava4-live-4.2.12+dfsg dpkg-source: info: unpacking biojava4-live_4.2.12+dfsg.orig.tar.xz dpkg-source: info: unpacking biojava4-live_4.2.12+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_itext_class_updates dpkg-source: info: applying use_simple_json dpkg-source: info: applying fix_import dpkg-source: info: applying faketest dpkg-source: info: applying fix_ascii_characters_mapping dpkg-source: info: applying skip_network_related_tests dpkg-source: info: applying remove_openchart_use dpkg-source: info: applying ignore_fake_tests I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3549/tmp/hooks/D01_modify_environment starting debug: Running on p64b. 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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/3549/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3549/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=4ec74a6417954995a782178afe4cac82 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=3549 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/tmp.Q7Cd4kUH2Y/pbuilderrc_oS2p --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Q7Cd4kUH2Y/b2 --logfile b2/build.log biojava4-live_4.2.12+dfsg-2.dsc' SUDO_GID=115 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2 (2020-04-29) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash -rwxr-xr-x 1 root root 71648 Mar 1 2019 date -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd -rwxr-xr-x 1 root root 55672 Mar 1 2019 df -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 18260 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln -rwxr-xr-x 1 root root 34932 Jul 27 2018 login -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 10 2019 more -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jun 11 05:50 sh -> bash lrwxrwxrwx 1 root root 4 Jun 10 22:26 sh.distrib -> dash -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty -rwsr-xr-x 1 root root 42472 Jan 10 2019 su -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch -rwxr-xr-x 1 root root 18260 Mar 1 2019 true -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/3549/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: armhf 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 (>= 11~), ant, libcommons-dbcp-java, libhsqldb-java, libcommons-collections3-java, libcommons-pool-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libguava-java (>= 17.0), libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java (>= 14.6.4), libvecmath-java, default-jdk-headless, junit4, javahelper, ant-optional, ant-contrib, libhamcrest-java, libjson-simple-java (>= 1.1.1), liblog4j2-java, libslf4j-java, libxmlunit-java, libjgrapht-java, libjaxb-api-java, libjaxb-java, libnetx-java, default-jdk-doc, rdfind dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on ant; however: Package ant is not installed. pbuilder-satisfydepends-dummy depends on libcommons-dbcp-java; however: Package libcommons-dbcp-java is not installed. pbuilder-satisfydepends-dummy depends on libhsqldb-java; however: Package libhsqldb-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-collections3-java; however: Package libcommons-collections3-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-pool-java; however: Package libcommons-pool-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-logging-java; however: Package libcommons-logging-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math-java; however: Package libcommons-math-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-cli-java; however: Package libcommons-cli-java is not installed. pbuilder-satisfydepends-dummy depends on libguava-java (>= 17.0); however: Package libguava-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-codec-java; however: Package libcommons-codec-java is not installed. pbuilder-satisfydepends-dummy depends on libitext5-java (>= 5.4.1); however: Package libitext5-java is not installed. pbuilder-satisfydepends-dummy depends on libjmol-java (>= 14.6.4); however: Package libjmol-java is not installed. pbuilder-satisfydepends-dummy depends on libvecmath-java; however: Package libvecmath-java is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-headless; however: Package default-jdk-headless is not installed. pbuilder-satisfydepends-dummy depends on junit4; however: Package junit4 is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on ant-optional; however: Package ant-optional is not installed. pbuilder-satisfydepends-dummy depends on ant-contrib; however: Package ant-contrib is not installed. pbuilder-satisfydepends-dummy depends on libhamcrest-java; however: Package libhamcrest-java is not installed. pbuilder-satisfydepends-dummy depends on libjson-simple-java (>= 1.1.1); however: Package libjson-simple-java is not installed. pbuilder-satisfydepends-dummy depends on liblog4j2-java; however: Package liblog4j2-java is not installed. pbuilder-satisfydepends-dummy depends on libslf4j-java; however: Package libslf4j-java is not installed. pbuilder-satisfydepends-dummy depends on libxmlunit-java; however: Package libxmlunit-java is not installed. pbuilder-satisfydepends-dummy depends on libjgrapht-java; however: Package libjgrapht-java is not installed. pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however: Package libjaxb-api-java is not installed. pbuilder-satisfydepends-dummy depends on libjaxb-java; however: Package libjaxb-java is not installed. pbuilder-satisfydepends-dummy depends on libnetx-java; however: Package libnetx-java is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-doc; however: Package default-jdk-doc is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind 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-contrib{a} ant-optional{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{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} 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} javahelper{a} junit{a} junit4{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-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} libbsd0{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libcodemodel-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-dbcp-java{a} libcommons-io-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-parent-java{a} libcommons-pool-java{a} libcroco3{a} libcups2{a} libdbus-1-3{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdom4j-java{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} libexpat1{a} libfastinfoset-java{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{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} libgssapi-krb5-2{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libhsqldb-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu63{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libitext5-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjgraph-java{a} libjgrapht0.8-java{a} libjmol-java{a} libjpeg62-turbo{a} libjson-simple-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} liblightcouch-java{a} liblog4j2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libmpdec2{a} libnaga-java{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnetx-java{a} libnpth0{a} libnspr4{a} libnss3{a} libparams-classify-perl{a} libpcsclite1{a} libpipeline1{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librelaxng-datatype-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libservlet-api-java{a} libservlet3.1-java{a} libsigsegv2{a} libsisu-guice-java{a} libsisu-inject-java{a} libsisu-ioc-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssl1.1{a} libstax-ex-java{a} libstreambuffer-java{a} libstrictures-perl{a} libsub-exporter-progressive-perl{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} liburi-perl{a} libvecmath-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxmlunit-java{a} libxrender1{a} libxsom-java{a} libxtst6{a} libxz-java{a} lsb-base{a} m4{a} man-db{a} mime-support{a} netbase{a} openjdk-11-doc{a} openjdk-11-jdk-headless{a} openjdk-11-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} ucf{a} wdiff{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: at curl dbus debian-keyring dput dput-ng dupload equivs krb5-locales libarchive-cpio-perl libasm-java libcglib-java libclass-xsaccessor-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libjansi-java liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libsub-name-perl licensecheck lintian lynx python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg shared-mime-info strace unzip wget xdg-user-dirs 0 packages upgraded, 243 newly installed, 0 to remove and 0 not upgraded. Need to get 309 MB of archives. After unpacking 805 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libpython3.7-minimal armhf 3.7.3-2+deb10u1 [582 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python3.7-minimal armhf 3.7.3-2+deb10u1 [1465 kB] Get: 11 http://deb.debian.org/debian buster/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libmpdec2 armhf 2.4.2-2 [69.3 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython3.7-stdlib armhf 3.7.3-2+deb10u1 [1660 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python3.7 armhf 3.7.3-2+deb10u1 [330 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB] Get: 19 http://deb.debian.org/debian buster/main armhf python3 armhf 3.7.3-1 [61.5 kB] Get: 20 http://deb.debian.org/debian buster/main armhf netbase all 5.6 [19.4 kB] Get: 21 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 24 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 25 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 26 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 27 http://deb.debian.org/debian buster/main armhf openssl armhf 1.1.1d-0+deb10u3 [818 kB] Get: 28 http://deb.debian.org/debian buster/main armhf ca-certificates all 20190110 [157 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libnspr4 armhf 2:4.20-1 [90.0 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libnss3 armhf 2:3.42.1-1+deb10u2 [969 kB] Get: 31 http://deb.debian.org/debian buster/main armhf ca-certificates-java all 20190405 [15.7 kB] Get: 32 http://deb.debian.org/debian buster/main armhf java-common all 0.71 [14.4 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libavahi-common-data armhf 0.7-4+b1 [122 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libavahi-common3 armhf 0.7-4+b1 [51.1 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libdbus-1-3 armhf 1.12.16-1 [190 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libavahi-client3 armhf 0.7-4+b1 [54.5 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libcups2 armhf 2.2.10-6+deb10u3 [291 kB] Get: 43 http://deb.debian.org/debian buster/main armhf liblcms2-2 armhf 2.9-3 [119 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [112 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 47 http://deb.debian.org/debian buster/main armhf fonts-dejavu-core all 2.37-1 [1068 kB] Get: 48 http://deb.debian.org/debian buster/main armhf fontconfig-config all 2.13.1-2 [280 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libfontconfig1 armhf 2.13.1-2 [328 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libasound2-data all 1.1.8-1 [59.6 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libasound2 armhf 1.1.8-1 [310 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libpcsclite1 armhf 1.8.24-1 [55.4 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libxcb1 armhf 1.13.1-2 [132 kB] Get: 56 http://deb.debian.org/debian buster/main armhf libx11-data all 2:1.6.7-1 [298 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libx11-6 armhf 2:1.6.7-1 [698 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libxext6 armhf 2:1.3.3-1+b2 [48.1 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libxi6 armhf 2:1.7.9-1 [78.4 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 61 http://deb.debian.org/debian buster/main armhf lsb-base all 10.2019051400 [28.4 kB] Get: 62 http://deb.debian.org/debian buster/main armhf x11-common all 1:7.7+19 [251 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB] Get: 64 http://deb.debian.org/debian buster/main armhf openjdk-11-jre-headless armhf 11.0.6+10-1~deb10u1 [33.2 MB] Get: 65 http://deb.debian.org/debian buster/main armhf default-jre-headless armhf 2:1.11-71 [10.9 kB] Get: 66 http://deb.debian.org/debian buster/main armhf ant all 1.10.5-2 [2082 kB] Get: 67 http://deb.debian.org/debian buster/main armhf ant-contrib all 1.0~b3+svn177-10 [262 kB] Get: 68 http://deb.debian.org/debian buster/main armhf ant-optional all 1.10.5-2 [379 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 70 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 71 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 72 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 73 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 74 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 75 http://deb.debian.org/debian buster/main armhf dctrl-tools armhf 2.24-3 [96.0 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 77 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 79 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 80 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 82 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 84 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 86 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 87 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 88 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 89 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 90 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 91 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 92 http://deb.debian.org/debian buster/main armhf openjdk-11-doc all 11.0.6+10-1~deb10u1 [13.5 MB] Get: 93 http://deb.debian.org/debian buster/main armhf default-jdk-doc armhf 2:1.11-71 [10.9 kB] Get: 94 http://deb.debian.org/debian buster/main armhf openjdk-11-jdk-headless armhf 11.0.6+10-1~deb10u1 [183 MB] Get: 95 http://deb.debian.org/debian buster/main armhf default-jdk-headless armhf 2:1.11-71 [1104 B] Get: 96 http://deb.debian.org/debian buster/main armhf libassuan0 armhf 2.5.2-1 [42.8 kB] Get: 97 http://deb.debian.org/debian buster/main armhf gpgconf armhf 2.2.12-1+deb10u1 [492 kB] Get: 98 http://deb.debian.org/debian buster/main armhf libksba8 armhf 1.3.5-2 [85.9 kB] Get: 99 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 100 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 101 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 102 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 103 http://deb.debian.org/debian buster/main armhf libnpth0 armhf 1.6-1 [17.4 kB] Get: 104 http://deb.debian.org/debian buster/main armhf dirmngr armhf 2.2.12-1+deb10u1 [669 kB] Get: 105 http://deb.debian.org/debian buster/main armhf gnupg-l10n all 2.2.12-1+deb10u1 [1010 kB] Get: 106 http://deb.debian.org/debian buster/main armhf gnupg-utils armhf 2.2.12-1+deb10u1 [788 kB] Get: 107 http://deb.debian.org/debian buster/main armhf gpg armhf 2.2.12-1+deb10u1 [804 kB] Get: 108 http://deb.debian.org/debian buster/main armhf pinentry-curses armhf 1.1.0-2 [59.8 kB] Get: 109 http://deb.debian.org/debian buster/main armhf gpg-agent armhf 2.2.12-1+deb10u1 [578 kB] Get: 110 http://deb.debian.org/debian buster/main armhf gpg-wks-client armhf 2.2.12-1+deb10u1 [469 kB] Get: 111 http://deb.debian.org/debian buster/main armhf gpg-wks-server armhf 2.2.12-1+deb10u1 [464 kB] Get: 112 http://deb.debian.org/debian buster/main armhf gpgsm armhf 2.2.12-1+deb10u1 [573 kB] Get: 113 http://deb.debian.org/debian buster/main armhf gnupg all 2.2.12-1+deb10u1 [715 kB] Get: 114 http://deb.debian.org/debian buster/main armhf libfile-which-perl all 1.23-1 [16.6 kB] Get: 115 http://deb.debian.org/debian buster/main armhf libfile-homedir-perl all 1.004-1 [42.7 kB] Get: 116 http://deb.debian.org/debian buster/main armhf libio-pty-perl armhf 1:1.08-1.1+b5 [32.9 kB] Get: 117 http://deb.debian.org/debian buster/main armhf libipc-run-perl all 20180523.0-1 [101 kB] Get: 118 http://deb.debian.org/debian buster/main armhf libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get: 119 http://deb.debian.org/debian buster/main armhf libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get: 120 http://deb.debian.org/debian buster/main armhf libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get: 121 http://deb.debian.org/debian buster/main armhf libb-hooks-op-check-perl armhf 0.22-1+b1 [11.0 kB] Get: 122 http://deb.debian.org/debian buster/main armhf libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get: 123 http://deb.debian.org/debian buster/main armhf libdevel-callchecker-perl armhf 0.008-1 [15.5 kB] Get: 124 http://deb.debian.org/debian buster/main armhf libparams-classify-perl armhf 0.015-1+b1 [24.2 kB] Get: 125 http://deb.debian.org/debian buster/main armhf libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 126 http://deb.debian.org/debian buster/main armhf libimport-into-perl all 1.002005-1 [11.6 kB] Get: 127 http://deb.debian.org/debian buster/main armhf librole-tiny-perl all 2.000006-1 [19.4 kB] Get: 128 http://deb.debian.org/debian buster/main armhf libstrictures-perl all 2.000005-1 [18.3 kB] Get: 129 http://deb.debian.org/debian buster/main armhf libsub-quote-perl all 2.005001-1 [17.9 kB] Get: 130 http://deb.debian.org/debian buster/main armhf libmoo-perl all 2.003004-2 [57.4 kB] Get: 131 http://deb.debian.org/debian buster/main armhf libencode-locale-perl all 1.05-1 [13.7 kB] Get: 132 http://deb.debian.org/debian buster/main armhf libtimedate-perl all 2.3000-2+deb10u1 [38.1 kB] Get: 133 http://deb.debian.org/debian buster/main armhf libhttp-date-perl all 6.02-1 [10.7 kB] Get: 134 http://deb.debian.org/debian buster/main armhf libfile-listing-perl all 6.04-1 [10.3 kB] Get: 135 http://deb.debian.org/debian buster/main armhf libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 136 http://deb.debian.org/debian buster/main armhf liburi-perl all 1.76-1 [89.9 kB] Get: 137 http://deb.debian.org/debian buster/main armhf libhtml-parser-perl armhf 3.72-3+b3 [102 kB] Get: 138 http://deb.debian.org/debian buster/main armhf libhtml-tree-perl all 5.07-2 [213 kB] Get: 139 http://deb.debian.org/debian buster/main armhf libio-html-perl all 1.001-1 [17.6 kB] Get: 140 http://deb.debian.org/debian buster/main armhf liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get: 141 http://deb.debian.org/debian buster/main armhf libhttp-message-perl all 6.18-1 [77.8 kB] Get: 142 http://deb.debian.org/debian buster/main armhf libhttp-cookies-perl all 6.04-1 [17.8 kB] Get: 143 http://deb.debian.org/debian buster/main armhf libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 144 http://deb.debian.org/debian buster/main armhf perl-openssl-defaults armhf 3 [6782 B] Get: 145 http://deb.debian.org/debian buster/main armhf libnet-ssleay-perl armhf 1.85-2+b1 [288 kB] Get: 146 http://deb.debian.org/debian buster/main armhf libio-socket-ssl-perl all 2.060-3 [207 kB] Get: 147 http://deb.debian.org/debian buster/main armhf libnet-http-perl all 6.18-1 [24.5 kB] Get: 148 http://deb.debian.org/debian buster/main armhf liblwp-protocol-https-perl all 6.07-2 [9242 B] Get: 149 http://deb.debian.org/debian buster/main armhf libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 150 http://deb.debian.org/debian buster/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 151 http://deb.debian.org/debian buster/main armhf libwww-perl all 6.36-2 [188 kB] Get: 152 http://deb.debian.org/debian buster/main armhf patchutils armhf 0.3.4-2 [86.2 kB] Get: 153 http://deb.debian.org/debian buster/main armhf wdiff armhf 1.2.2-2+b1 [121 kB] Get: 154 http://deb.debian.org/debian buster/main armhf devscripts armhf 2.19.5+deb10u1 [1045 kB] Get: 155 http://deb.debian.org/debian buster/main armhf javahelper all 0.72.9 [96.4 kB] Get: 156 http://deb.debian.org/debian buster/main armhf junit all 3.8.2-9 [110 kB] Get: 157 http://deb.debian.org/debian buster/main armhf libhamcrest-java all 1.3-9 [388 kB] Get: 158 http://deb.debian.org/debian buster/main armhf junit4 all 4.12-8 [292 kB] Get: 159 http://deb.debian.org/debian buster/main armhf libactivation-java all 1.2.0-2 [84.7 kB] Get: 160 http://deb.debian.org/debian buster/main armhf libaopalliance-java all 20070526-6 [9048 B] Get: 161 http://deb.debian.org/debian buster/main armhf libapache-pom-java all 18-1 [4676 B] Get: 162 http://deb.debian.org/debian buster/main armhf libargs4j-java all 2.33-1 [139 kB] Get: 163 http://deb.debian.org/debian buster/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 164 http://deb.debian.org/debian buster/main armhf libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 165 http://deb.debian.org/debian buster/main armhf libcdi-api-java all 1.2-2 [54.5 kB] Get: 166 http://deb.debian.org/debian buster/main armhf libjaxen-java all 1.1.6-4 [214 kB] Get: 167 http://deb.debian.org/debian buster/main armhf libdom4j-java all 2.1.1-2 [310 kB] Get: 168 http://deb.debian.org/debian buster/main armhf libcommons-parent-java all 43-1 [10.8 kB] Get: 169 http://deb.debian.org/debian buster/main armhf libcommons-io-java all 2.6-2 [213 kB] Get: 170 http://deb.debian.org/debian buster/main armhf libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 171 http://deb.debian.org/debian buster/main armhf libcommons-cli-java all 1.4-1 [55.2 kB] Get: 172 http://deb.debian.org/debian buster/main armhf libcommons-lang3-java all 3.8-2 [478 kB] Get: 173 http://deb.debian.org/debian buster/main armhf libgeronimo-annotation-1.3-spec-java all 1.0-1 [10.6 kB] Get: 174 http://deb.debian.org/debian buster/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 175 http://deb.debian.org/debian buster/main armhf libguava-java all 19.0-1 [2028 kB] Get: 176 http://deb.debian.org/debian buster/main armhf libguice-java all 4.2.1-1 [962 kB] Get: 177 http://deb.debian.org/debian buster/main armhf libmaven-parent-java all 31-2 [5100 B] Get: 178 http://deb.debian.org/debian buster/main armhf libplexus-utils2-java all 3.1.1-1 [249 kB] Get: 179 http://deb.debian.org/debian buster/main armhf libwagon-provider-api-java all 3.3.1-2 [50.1 kB] Get: 180 http://deb.debian.org/debian buster/main armhf libmaven-resolver-java all 1.3.1-1 [549 kB] Get: 181 http://deb.debian.org/debian buster/main armhf libplexus-cipher-java all 1.7-3 [15.0 kB] Get: 182 http://deb.debian.org/debian buster/main armhf libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 183 http://deb.debian.org/debian buster/main armhf libplexus-component-annotations-java all 1.7.1-7 [7536 B] Get: 184 http://deb.debian.org/debian buster/main armhf libplexus-interpolation-java all 1.25-1 [76.8 kB] Get: 185 http://deb.debian.org/debian buster/main armhf libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 186 http://deb.debian.org/debian buster/main armhf libslf4j-java all 1.7.25-3 [143 kB] Get: 187 http://deb.debian.org/debian buster/main armhf libsisu-inject-java all 0.3.3-1 [347 kB] Get: 188 http://deb.debian.org/debian buster/main armhf libsisu-plexus-java all 0.3.3-3 [182 kB] Get: 189 http://deb.debian.org/debian buster/main armhf libmaven3-core-java all 3.6.0-1 [1465 kB] Get: 190 http://deb.debian.org/debian buster/main armhf libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 191 http://deb.debian.org/debian buster/main armhf libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 192 http://deb.debian.org/debian buster/main armhf libcommons-compress-java all 1.18-2 [530 kB] Get: 193 http://deb.debian.org/debian buster/main armhf libplexus-io-java all 3.1.1-1 [64.6 kB] Get: 194 http://deb.debian.org/debian buster/main armhf libsnappy1v5 armhf 1.1.7-1 [15.2 kB] Get: 195 http://deb.debian.org/debian buster/main armhf libsnappy-jni armhf 1.1.7.2-1 [6784 B] Get: 196 http://deb.debian.org/debian buster/main armhf libsnappy-java all 1.1.7.2-1 [73.7 kB] Get: 197 http://deb.debian.org/debian buster/main armhf libxz-java all 1.8-2 [141 kB] Get: 198 http://deb.debian.org/debian buster/main armhf libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 199 http://deb.debian.org/debian buster/main armhf libsisu-guice-java all 4.2.0-1 [785 kB] Get: 200 http://deb.debian.org/debian buster/main armhf libsisu-ioc-java all 2.3.0-11 [492 kB] Get: 201 http://deb.debian.org/debian buster/main armhf libhttpcore-java all 4.4.11-1 [625 kB] Get: 202 http://deb.debian.org/debian buster/main armhf libcommons-codec-java all 1.11-1 [271 kB] Get: 203 http://deb.debian.org/debian buster/main armhf libcommons-logging-java all 1.2-2 [62.2 kB] Get: 204 http://deb.debian.org/debian buster/main armhf libhttpclient-java all 4.5.7-1 [721 kB] Get: 205 http://deb.debian.org/debian buster/main armhf libjsoup-java all 1.10.2-2 [350 kB] Get: 206 http://deb.debian.org/debian buster/main armhf libwagon-http-java all 3.3.1-2 [50.5 kB] Get: 207 http://deb.debian.org/debian buster/main armhf libistack-commons-java all 3.0.6-3 [144 kB] Get: 208 http://deb.debian.org/debian buster/main armhf libcodemodel-java all 2.6+jaxb2.3.0.1-8 [163 kB] Get: 209 http://deb.debian.org/debian buster/main armhf libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 210 http://deb.debian.org/debian buster/main armhf libcommons-pool-java all 1.6-3 [104 kB] Get: 211 http://deb.debian.org/debian buster/main armhf libcommons-dbcp-java all 1.4-6 [157 kB] Get: 212 http://deb.debian.org/debian buster/main armhf libcommons-math-java all 2.2-7 [928 kB] Get: 213 http://deb.debian.org/debian buster/main armhf libdtd-parser-java all 1.2~svn20110404-1 [62.5 kB] Get: 214 http://deb.debian.org/debian buster/main armhf libel-api-java all 3.0.0-2+deb10u1 [64.9 kB] Get: 215 http://deb.debian.org/debian buster/main armhf libjaxb-api-java all 2.3.1-1 [119 kB] Get: 216 http://deb.debian.org/debian buster/main armhf libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 217 http://deb.debian.org/debian buster/main armhf libstreambuffer-java all 1.5.4-1 [71.8 kB] Get: 218 http://deb.debian.org/debian buster/main armhf librelaxng-datatype-java all 1.0+ds1-3 [11.7 kB] Get: 219 http://deb.debian.org/debian buster/main armhf libxsom-java all 2.3.0.1-8 [396 kB] Get: 220 http://deb.debian.org/debian buster/main armhf libfastinfoset-java all 1.2.12-3 [343 kB] Get: 221 http://deb.debian.org/debian buster/main armhf libgoogle-gson-java all 2.8.5-3 [225 kB] Get: 222 http://deb.debian.org/debian buster/main armhf libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 223 http://deb.debian.org/debian buster/main armhf libjsp-api-java all 2.3.4-2+deb10u1 [53.7 kB] Get: 224 http://deb.debian.org/debian buster/main armhf libwebsocket-api-java all 1.1-1+deb10u1 [40.0 kB] Get: 225 http://deb.debian.org/debian buster/main armhf libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 226 http://deb.debian.org/debian buster/main armhf libhsqldb-java all 2.4.1-2 [1633 kB] Get: 227 http://deb.debian.org/debian buster/main armhf libitext5-java all 5.5.13-1 [2620 kB] Get: 228 http://deb.debian.org/debian buster/main armhf librngom-java all 2.3.0.1-8 [288 kB] Get: 229 http://deb.debian.org/debian buster/main armhf libtxw2-java all 2.3.0.1-8 [134 kB] Get: 230 http://deb.debian.org/debian buster/main armhf libxml-commons-resolver1.1-java all 1.2-9 [91.6 kB] Get: 231 http://deb.debian.org/debian buster/main armhf libjaxb-java all 2.3.0.1-8 [1966 kB] Get: 232 http://deb.debian.org/debian buster/main armhf libjaxp1.3-java all 1.3.05-5 [226 kB] Get: 233 http://deb.debian.org/debian buster/main armhf libjgraph-java all 5.12.4.2+dfsg-5 [205 kB] Get: 234 http://deb.debian.org/debian buster/main armhf libjgrapht0.8-java all 0.8.3-5 [214 kB] Get: 235 http://deb.debian.org/debian buster/main armhf libnaga-java all 3.0+svn80-2 [884 kB] Get: 236 http://deb.debian.org/debian buster/main armhf libjmol-java all 14.6.4+2016.11.05+dfsg1-4 [6393 kB] Get: 237 http://deb.debian.org/debian buster/main armhf libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 238 http://deb.debian.org/debian buster/main armhf liblightcouch-java all 0.0.6-1 [63.7 kB] Get: 239 http://deb.debian.org/debian buster/main armhf liblog4j2-java all 2.11.1-2 [1721 kB] Get: 240 http://deb.debian.org/debian buster/main armhf libnetx-java all 0.5-4 [138 kB] Get: 241 http://deb.debian.org/debian buster/main armhf libvecmath-java all 1.5.2-7 [97.0 kB] Get: 242 http://deb.debian.org/debian buster/main armhf libxmlunit-java all 1.6-1 [95.5 kB] Get: 243 http://deb.debian.org/debian buster/main armhf rdfind armhf 1.4.1-1 [36.3 kB] Fetched 309 MB in 41s (7604 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../1-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../2-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../3-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../4-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../5-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../6-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package libpython3.7-minimal:armhf. Preparing to unpack .../7-libpython3.7-minimal_3.7.3-2+deb10u1_armhf.deb ... Unpacking libpython3.7-minimal:armhf (3.7.3-2+deb10u1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../8-libexpat1_2.2.6-2+deb10u1_armhf.deb ... Unpacking libexpat1:armhf (2.2.6-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../9-python3.7-minimal_3.7.3-2+deb10u1_armhf.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u1) ... Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libpython3.7-minimal:armhf (3.7.3-2+deb10u1) ... Setting up libexpat1:armhf (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u1) ... 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 ... 19827 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.3-1_armhf.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libmpdec2:armhf. Preparing to unpack .../2-libmpdec2_2.4.2-2_armhf.deb ... Unpacking libmpdec2:armhf (2.4.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:armhf. Preparing to unpack .../4-libreadline7_7.0-5_armhf.deb ... Unpacking libreadline7:armhf (7.0-5) ... Selecting previously unselected package libpython3.7-stdlib:armhf. Preparing to unpack .../5-libpython3.7-stdlib_3.7.3-2+deb10u1_armhf.deb ... Unpacking libpython3.7-stdlib:armhf (3.7.3-2+deb10u1) ... Selecting previously unselected package python3.7. Preparing to unpack .../6-python3.7_3.7.3-2+deb10u1_armhf.deb ... Unpacking python3.7 (3.7.3-2+deb10u1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../7-libpython3-stdlib_3.7.3-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20288 files and directories currently installed.) Preparing to unpack .../000-python3_3.7.3-1_armhf.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../004-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../007-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../008-openssl_1.1.1d-0+deb10u3_armhf.deb ... Unpacking openssl (1.1.1d-0+deb10u3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../009-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) ... Selecting previously unselected package libnspr4:armhf. Preparing to unpack .../010-libnspr4_2%3a4.20-1_armhf.deb ... Unpacking libnspr4:armhf (2:4.20-1) ... Selecting previously unselected package libnss3:armhf. Preparing to unpack .../011-libnss3_2%3a3.42.1-1+deb10u2_armhf.deb ... Unpacking libnss3:armhf (2:3.42.1-1+deb10u2) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../012-ca-certificates-java_20190405_all.deb ... Unpacking ca-certificates-java (20190405) ... Selecting previously unselected package java-common. Preparing to unpack .../013-java-common_0.71_all.deb ... Unpacking java-common (0.71) ... Selecting previously unselected package libavahi-common-data:armhf. Preparing to unpack .../014-libavahi-common-data_0.7-4+b1_armhf.deb ... Unpacking libavahi-common-data:armhf (0.7-4+b1) ... Selecting previously unselected package libavahi-common3:armhf. Preparing to unpack .../015-libavahi-common3_0.7-4+b1_armhf.deb ... Unpacking libavahi-common3:armhf (0.7-4+b1) ... Selecting previously unselected package libdbus-1-3:armhf. Preparing to unpack .../016-libdbus-1-3_1.12.16-1_armhf.deb ... Unpacking libdbus-1-3:armhf (1.12.16-1) ... Selecting previously unselected package libavahi-client3:armhf. Preparing to unpack .../017-libavahi-client3_0.7-4+b1_armhf.deb ... Unpacking libavahi-client3:armhf (0.7-4+b1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../018-libkeyutils1_1.6-6_armhf.deb ... Unpacking libkeyutils1:armhf (1.6-6) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../019-libkrb5support0_1.17-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.17-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../020-libk5crypto3_1.17-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.17-3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../021-libkrb5-3_1.17-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../022-libgssapi-krb5-2_1.17-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.17-3) ... Selecting previously unselected package libcups2:armhf. Preparing to unpack .../023-libcups2_2.2.10-6+deb10u3_armhf.deb ... Unpacking libcups2:armhf (2.2.10-6+deb10u3) ... Selecting previously unselected package liblcms2-2:armhf. Preparing to unpack .../024-liblcms2-2_2.9-3_armhf.deb ... Unpacking liblcms2-2:armhf (2.9-3) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../025-libjpeg62-turbo_1%3a1.5.2-2+b1_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:1.5.2-2+b1) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../026-libpng16-16_1.6.36-6_armhf.deb ... Unpacking libpng16-16:armhf (1.6.36-6) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../027-libfreetype6_2.9.1-3+deb10u1_armhf.deb ... Unpacking libfreetype6:armhf (2.9.1-3+deb10u1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../028-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../029-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../030-libfontconfig1_2.13.1-2_armhf.deb ... Unpacking libfontconfig1:armhf (2.13.1-2) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../031-libasound2-data_1.1.8-1_all.deb ... Unpacking libasound2-data (1.1.8-1) ... Selecting previously unselected package libasound2:armhf. Preparing to unpack .../032-libasound2_1.1.8-1_armhf.deb ... Unpacking libasound2:armhf (1.1.8-1) ... Selecting previously unselected package libpcsclite1:armhf. Preparing to unpack .../033-libpcsclite1_1.8.24-1_armhf.deb ... Unpacking libpcsclite1:armhf (1.8.24-1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../034-libxau6_1%3a1.0.8-1+b2_armhf.deb ... Unpacking libxau6:armhf (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../035-libxdmcp6_1%3a1.1.2-3_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../036-libxcb1_1.13.1-2_armhf.deb ... Unpacking libxcb1:armhf (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../037-libx11-data_2%3a1.6.7-1_all.deb ... Unpacking libx11-data (2:1.6.7-1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../038-libx11-6_2%3a1.6.7-1_armhf.deb ... Unpacking libx11-6:armhf (2:1.6.7-1) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../039-libxext6_2%3a1.3.3-1+b2_armhf.deb ... Unpacking libxext6:armhf (2:1.3.3-1+b2) ... Selecting previously unselected package libxi6:armhf. Preparing to unpack .../040-libxi6_2%3a1.7.9-1_armhf.deb ... Unpacking libxi6:armhf (2:1.7.9-1) ... Selecting previously unselected package libxrender1:armhf. Preparing to unpack .../041-libxrender1_1%3a0.9.10-1_armhf.deb ... Unpacking libxrender1:armhf (1:0.9.10-1) ... Selecting previously unselected package lsb-base. Preparing to unpack .../042-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package x11-common. Preparing to unpack .../043-x11-common_1%3a7.7+19_all.deb ... Unpacking x11-common (1:7.7+19) ... Selecting previously unselected package libxtst6:armhf. Preparing to unpack .../044-libxtst6_2%3a1.2.3-1_armhf.deb ... Unpacking libxtst6:armhf (2:1.2.3-1) ... Selecting previously unselected package openjdk-11-jre-headless:armhf. Preparing to unpack .../045-openjdk-11-jre-headless_11.0.6+10-1~deb10u1_armhf.deb ... Unpacking openjdk-11-jre-headless:armhf (11.0.6+10-1~deb10u1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../046-default-jre-headless_2%3a1.11-71_armhf.deb ... Unpacking default-jre-headless (2:1.11-71) ... Selecting previously unselected package ant. Preparing to unpack .../047-ant_1.10.5-2_all.deb ... Unpacking ant (1.10.5-2) ... Selecting previously unselected package ant-contrib. Preparing to unpack .../048-ant-contrib_1.0~b3+svn177-10_all.deb ... Unpacking ant-contrib (1.0~b3+svn177-10) ... Selecting previously unselected package ant-optional. Preparing to unpack .../049-ant-optional_1.10.5-2_all.deb ... Unpacking ant-optional (1.10.5-2) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../050-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../051-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../052-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../053-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../054-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../055-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../056-dctrl-tools_2.24-3_armhf.deb ... Unpacking dctrl-tools (2.24-3) ... Selecting previously unselected package libtool. Preparing to unpack .../057-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../058-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../059-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../060-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../061-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../062-libelf1_0.176-1.1_armhf.deb ... Unpacking libelf1:armhf (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../063-dwz_0.12-3_armhf.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../064-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../065-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../066-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../067-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../068-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../069-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../070-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../071-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../072-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package openjdk-11-doc. Preparing to unpack .../073-openjdk-11-doc_11.0.6+10-1~deb10u1_all.deb ... Unpacking openjdk-11-doc (11.0.6+10-1~deb10u1) ... Selecting previously unselected package default-jdk-doc. Preparing to unpack .../074-default-jdk-doc_2%3a1.11-71_armhf.deb ... Unpacking default-jdk-doc (2:1.11-71) ... Selecting previously unselected package openjdk-11-jdk-headless:armhf. Preparing to unpack .../075-openjdk-11-jdk-headless_11.0.6+10-1~deb10u1_armhf.deb ... Unpacking openjdk-11-jdk-headless:armhf (11.0.6+10-1~deb10u1) ... Selecting previously unselected package default-jdk-headless. Preparing to unpack .../076-default-jdk-headless_2%3a1.11-71_armhf.deb ... Unpacking default-jdk-headless (2:1.11-71) ... Selecting previously unselected package libassuan0:armhf. Preparing to unpack .../077-libassuan0_2.5.2-1_armhf.deb ... Unpacking libassuan0:armhf (2.5.2-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../078-gpgconf_2.2.12-1+deb10u1_armhf.deb ... Unpacking gpgconf (2.2.12-1+deb10u1) ... Selecting previously unselected package libksba8:armhf. Preparing to unpack .../079-libksba8_1.3.5-2_armhf.deb ... Unpacking libksba8:armhf (1.3.5-2) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../080-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../081-libsasl2-2_2.1.27+dfsg-1+deb10u1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../082-libldap-common_2.4.47+dfsg-3+deb10u2_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../083-libldap-2.4-2_2.4.47+dfsg-3+deb10u2_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libnpth0:armhf. Preparing to unpack .../084-libnpth0_1.6-1_armhf.deb ... Unpacking libnpth0:armhf (1.6-1) ... Selecting previously unselected package dirmngr. Preparing to unpack .../085-dirmngr_2.2.12-1+deb10u1_armhf.deb ... Unpacking dirmngr (2.2.12-1+deb10u1) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../086-gnupg-l10n_2.2.12-1+deb10u1_all.deb ... Unpacking gnupg-l10n (2.2.12-1+deb10u1) ... Selecting previously unselected package gnupg-utils. Preparing to unpack .../087-gnupg-utils_2.2.12-1+deb10u1_armhf.deb ... Unpacking gnupg-utils (2.2.12-1+deb10u1) ... Selecting previously unselected package gpg. Preparing to unpack .../088-gpg_2.2.12-1+deb10u1_armhf.deb ... Unpacking gpg (2.2.12-1+deb10u1) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../089-pinentry-curses_1.1.0-2_armhf.deb ... Unpacking pinentry-curses (1.1.0-2) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../090-gpg-agent_2.2.12-1+deb10u1_armhf.deb ... Unpacking gpg-agent (2.2.12-1+deb10u1) ... Selecting previously unselected package gpg-wks-client. Preparing to unpack .../091-gpg-wks-client_2.2.12-1+deb10u1_armhf.deb ... Unpacking gpg-wks-client (2.2.12-1+deb10u1) ... Selecting previously unselected package gpg-wks-server. Preparing to unpack .../092-gpg-wks-server_2.2.12-1+deb10u1_armhf.deb ... Unpacking gpg-wks-server (2.2.12-1+deb10u1) ... Selecting previously unselected package gpgsm. Preparing to unpack .../093-gpgsm_2.2.12-1+deb10u1_armhf.deb ... Unpacking gpgsm (2.2.12-1+deb10u1) ... Selecting previously unselected package gnupg. Preparing to unpack .../094-gnupg_2.2.12-1+deb10u1_all.deb ... Unpacking gnupg (2.2.12-1+deb10u1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../095-libfile-which-perl_1.23-1_all.deb ... Unpacking libfile-which-perl (1.23-1) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../096-libfile-homedir-perl_1.004-1_all.deb ... Unpacking libfile-homedir-perl (1.004-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../097-libio-pty-perl_1%3a1.08-1.1+b5_armhf.deb ... Unpacking libio-pty-perl (1:1.08-1.1+b5) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../098-libipc-run-perl_20180523.0-1_all.deb ... Unpacking libipc-run-perl (20180523.0-1) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../099-libclass-method-modifiers-perl_2.12-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.12-1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../100-libsub-exporter-progressive-perl_0.001013-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-1) ... Selecting previously unselected package libdevel-globaldestruction-perl. Preparing to unpack .../101-libdevel-globaldestruction-perl_0.14-1_all.deb ... Unpacking libdevel-globaldestruction-perl (0.14-1) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../102-libb-hooks-op-check-perl_0.22-1+b1_armhf.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../103-libdynaloader-functions-perl_0.003-1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../104-libdevel-callchecker-perl_0.008-1_armhf.deb ... Unpacking libdevel-callchecker-perl (0.008-1) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../105-libparams-classify-perl_0.015-1+b1_armhf.deb ... Unpacking libparams-classify-perl (0.015-1+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../106-libmodule-runtime-perl_0.016-1_all.deb ... Unpacking libmodule-runtime-perl (0.016-1) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../107-libimport-into-perl_1.002005-1_all.deb ... Unpacking libimport-into-perl (1.002005-1) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../108-librole-tiny-perl_2.000006-1_all.deb ... Unpacking librole-tiny-perl (2.000006-1) ... Selecting previously unselected package libstrictures-perl. Preparing to unpack .../109-libstrictures-perl_2.000005-1_all.deb ... Unpacking libstrictures-perl (2.000005-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../110-libsub-quote-perl_2.005001-1_all.deb ... Unpacking libsub-quote-perl (2.005001-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../111-libmoo-perl_2.003004-2_all.deb ... Unpacking libmoo-perl (2.003004-2) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../112-libencode-locale-perl_1.05-1_all.deb ... Unpacking libencode-locale-perl (1.05-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../113-libtimedate-perl_2.3000-2+deb10u1_all.deb ... Unpacking libtimedate-perl (2.3000-2+deb10u1) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../114-libhttp-date-perl_6.02-1_all.deb ... Unpacking libhttp-date-perl (6.02-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../115-libfile-listing-perl_6.04-1_all.deb ... Unpacking libfile-listing-perl (6.04-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../116-libhtml-tagset-perl_3.20-3_all.deb ... Unpacking libhtml-tagset-perl (3.20-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../117-liburi-perl_1.76-1_all.deb ... Unpacking liburi-perl (1.76-1) ... Selecting previously unselected package libhtml-parser-perl. Preparing to unpack .../118-libhtml-parser-perl_3.72-3+b3_armhf.deb ... Unpacking libhtml-parser-perl (3.72-3+b3) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../119-libhtml-tree-perl_5.07-2_all.deb ... Unpacking libhtml-tree-perl (5.07-2) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../120-libio-html-perl_1.001-1_all.deb ... Unpacking libio-html-perl (1.001-1) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../121-liblwp-mediatypes-perl_6.02-1_all.deb ... Unpacking liblwp-mediatypes-perl (6.02-1) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../122-libhttp-message-perl_6.18-1_all.deb ... Unpacking libhttp-message-perl (6.18-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../123-libhttp-cookies-perl_6.04-1_all.deb ... Unpacking libhttp-cookies-perl (6.04-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../124-libhttp-negotiate-perl_6.01-1_all.deb ... Unpacking libhttp-negotiate-perl (6.01-1) ... Selecting previously unselected package perl-openssl-defaults:armhf. Preparing to unpack .../125-perl-openssl-defaults_3_armhf.deb ... Unpacking perl-openssl-defaults:armhf (3) ... Selecting previously unselected package libnet-ssleay-perl. Preparing to unpack .../126-libnet-ssleay-perl_1.85-2+b1_armhf.deb ... Unpacking libnet-ssleay-perl (1.85-2+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../127-libio-socket-ssl-perl_2.060-3_all.deb ... Unpacking libio-socket-ssl-perl (2.060-3) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../128-libnet-http-perl_6.18-1_all.deb ... Unpacking libnet-http-perl (6.18-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../129-liblwp-protocol-https-perl_6.07-2_all.deb ... Unpacking liblwp-protocol-https-perl (6.07-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../130-libtry-tiny-perl_0.30-1_all.deb ... Unpacking libtry-tiny-perl (0.30-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../131-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../132-libwww-perl_6.36-2_all.deb ... Unpacking libwww-perl (6.36-2) ... Selecting previously unselected package patchutils. Preparing to unpack .../133-patchutils_0.3.4-2_armhf.deb ... Unpacking patchutils (0.3.4-2) ... Selecting previously unselected package wdiff. Preparing to unpack .../134-wdiff_1.2.2-2+b1_armhf.deb ... Unpacking wdiff (1.2.2-2+b1) ... Selecting previously unselected package devscripts. Preparing to unpack .../135-devscripts_2.19.5+deb10u1_armhf.deb ... Unpacking devscripts (2.19.5+deb10u1) ... Selecting previously unselected package javahelper. Preparing to unpack .../136-javahelper_0.72.9_all.deb ... Unpacking javahelper (0.72.9) ... Selecting previously unselected package junit. Preparing to unpack .../137-junit_3.8.2-9_all.deb ... Unpacking junit (3.8.2-9) ... Selecting previously unselected package libhamcrest-java. Preparing to unpack .../138-libhamcrest-java_1.3-9_all.deb ... Unpacking libhamcrest-java (1.3-9) ... Selecting previously unselected package junit4. Preparing to unpack .../139-junit4_4.12-8_all.deb ... Unpacking junit4 (4.12-8) ... Selecting previously unselected package libactivation-java. Preparing to unpack .../140-libactivation-java_1.2.0-2_all.deb ... Unpacking libactivation-java (1.2.0-2) ... Selecting previously unselected package libaopalliance-java. Preparing to unpack .../141-libaopalliance-java_20070526-6_all.deb ... Unpacking libaopalliance-java (20070526-6) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../142-libapache-pom-java_18-1_all.deb ... Unpacking libapache-pom-java (18-1) ... Selecting previously unselected package libargs4j-java. Preparing to unpack .../143-libargs4j-java_2.33-1_all.deb ... Unpacking libargs4j-java (2.33-1) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../144-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ... Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java. Preparing to unpack .../145-libgeronimo-interceptor-3.0-spec-java_1.0.1-4_all.deb ... Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Selecting previously unselected package libcdi-api-java. Preparing to unpack .../146-libcdi-api-java_1.2-2_all.deb ... Unpacking libcdi-api-java (1.2-2) ... Selecting previously unselected package libjaxen-java. Preparing to unpack .../147-libjaxen-java_1.1.6-4_all.deb ... Unpacking libjaxen-java (1.1.6-4) ... Selecting previously unselected package libdom4j-java. Preparing to unpack .../148-libdom4j-java_2.1.1-2_all.deb ... Unpacking libdom4j-java (2.1.1-2) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../149-libcommons-parent-java_43-1_all.deb ... Unpacking libcommons-parent-java (43-1) ... Selecting previously unselected package libcommons-io-java. Preparing to unpack .../150-libcommons-io-java_2.6-2_all.deb ... Unpacking libcommons-io-java (2.6-2) ... Selecting previously unselected package libmaven-shared-utils-java. Preparing to unpack .../151-libmaven-shared-utils-java_3.3.0-1_all.deb ... Unpacking libmaven-shared-utils-java (3.3.0-1) ... Selecting previously unselected package libcommons-cli-java. Preparing to unpack .../152-libcommons-cli-java_1.4-1_all.deb ... Unpacking libcommons-cli-java (1.4-1) ... Selecting previously unselected package libcommons-lang3-java. Preparing to unpack .../153-libcommons-lang3-java_3.8-2_all.deb ... Unpacking libcommons-lang3-java (3.8-2) ... Selecting previously unselected package libgeronimo-annotation-1.3-spec-java. Preparing to unpack .../154-libgeronimo-annotation-1.3-spec-java_1.0-1_all.deb ... Unpacking libgeronimo-annotation-1.3-spec-java (1.0-1) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../155-libjsr305-java_0.1~+svn49-11_all.deb ... Unpacking libjsr305-java (0.1~+svn49-11) ... Selecting previously unselected package libguava-java. Preparing to unpack .../156-libguava-java_19.0-1_all.deb ... Unpacking libguava-java (19.0-1) ... Selecting previously unselected package libguice-java. Preparing to unpack .../157-libguice-java_4.2.1-1_all.deb ... Unpacking libguice-java (4.2.1-1) ... Selecting previously unselected package libmaven-parent-java. Preparing to unpack .../158-libmaven-parent-java_31-2_all.deb ... Unpacking libmaven-parent-java (31-2) ... Selecting previously unselected package libplexus-utils2-java. Preparing to unpack .../159-libplexus-utils2-java_3.1.1-1_all.deb ... Unpacking libplexus-utils2-java (3.1.1-1) ... Selecting previously unselected package libwagon-provider-api-java. Preparing to unpack .../160-libwagon-provider-api-java_3.3.1-2_all.deb ... Unpacking libwagon-provider-api-java (3.3.1-2) ... Selecting previously unselected package libmaven-resolver-java. Preparing to unpack .../161-libmaven-resolver-java_1.3.1-1_all.deb ... Unpacking libmaven-resolver-java (1.3.1-1) ... Selecting previously unselected package libplexus-cipher-java. Preparing to unpack .../162-libplexus-cipher-java_1.7-3_all.deb ... Unpacking libplexus-cipher-java (1.7-3) ... Selecting previously unselected package libplexus-classworlds-java. Preparing to unpack .../163-libplexus-classworlds-java_2.6.0-1_all.deb ... Unpacking libplexus-classworlds-java (2.6.0-1) ... Selecting previously unselected package libplexus-component-annotations-java. Preparing to unpack .../164-libplexus-component-annotations-java_1.7.1-7_all.deb ... Unpacking libplexus-component-annotations-java (1.7.1-7) ... Selecting previously unselected package libplexus-interpolation-java. Preparing to unpack .../165-libplexus-interpolation-java_1.25-1_all.deb ... Unpacking libplexus-interpolation-java (1.25-1) ... Selecting previously unselected package libplexus-sec-dispatcher-java. Preparing to unpack .../166-libplexus-sec-dispatcher-java_1.4-4_all.deb ... Unpacking libplexus-sec-dispatcher-java (1.4-4) ... Selecting previously unselected package libslf4j-java. Preparing to unpack .../167-libslf4j-java_1.7.25-3_all.deb ... Unpacking libslf4j-java (1.7.25-3) ... Selecting previously unselected package libsisu-inject-java. Preparing to unpack .../168-libsisu-inject-java_0.3.3-1_all.deb ... Unpacking libsisu-inject-java (0.3.3-1) ... Selecting previously unselected package libsisu-plexus-java. Preparing to unpack .../169-libsisu-plexus-java_0.3.3-3_all.deb ... Unpacking libsisu-plexus-java (0.3.3-3) ... Selecting previously unselected package libmaven3-core-java. Preparing to unpack .../170-libmaven3-core-java_3.6.0-1_all.deb ... Unpacking libmaven3-core-java (3.6.0-1) ... Selecting previously unselected package libmaven-shared-io-java. Preparing to unpack .../171-libmaven-shared-io-java_3.0.0-3_all.deb ... Unpacking libmaven-shared-io-java (3.0.0-3) ... Selecting previously unselected package libmaven-file-management-java. Preparing to unpack .../172-libmaven-file-management-java_3.0.0-1_all.deb ... Unpacking libmaven-file-management-java (3.0.0-1) ... Selecting previously unselected package libcommons-compress-java. Preparing to unpack .../173-libcommons-compress-java_1.18-2_all.deb ... Unpacking libcommons-compress-java (1.18-2) ... Selecting previously unselected package libplexus-io-java. Preparing to unpack .../174-libplexus-io-java_3.1.1-1_all.deb ... Unpacking libplexus-io-java (3.1.1-1) ... Selecting previously unselected package libsnappy1v5:armhf. Preparing to unpack .../175-libsnappy1v5_1.1.7-1_armhf.deb ... Unpacking libsnappy1v5:armhf (1.1.7-1) ... Selecting previously unselected package libsnappy-jni. Preparing to unpack .../176-libsnappy-jni_1.1.7.2-1_armhf.deb ... Unpacking libsnappy-jni (1.1.7.2-1) ... Selecting previously unselected package libsnappy-java. Preparing to unpack .../177-libsnappy-java_1.1.7.2-1_all.deb ... Unpacking libsnappy-java (1.1.7.2-1) ... Selecting previously unselected package libxz-java. Preparing to unpack .../178-libxz-java_1.8-2_all.deb ... Unpacking libxz-java (1.8-2) ... Selecting previously unselected package libplexus-archiver-java. Preparing to unpack .../179-libplexus-archiver-java_3.6.0-2_all.deb ... Unpacking libplexus-archiver-java (3.6.0-2) ... Selecting previously unselected package libsisu-guice-java. Preparing to unpack .../180-libsisu-guice-java_4.2.0-1_all.deb ... Unpacking libsisu-guice-java (4.2.0-1) ... Selecting previously unselected package libsisu-ioc-java. Preparing to unpack .../181-libsisu-ioc-java_2.3.0-11_all.deb ... Unpacking libsisu-ioc-java (2.3.0-11) ... Selecting previously unselected package libhttpcore-java. Preparing to unpack .../182-libhttpcore-java_4.4.11-1_all.deb ... Unpacking libhttpcore-java (4.4.11-1) ... Selecting previously unselected package libcommons-codec-java. Preparing to unpack .../183-libcommons-codec-java_1.11-1_all.deb ... Unpacking libcommons-codec-java (1.11-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../184-libcommons-logging-java_1.2-2_all.deb ... Unpacking libcommons-logging-java (1.2-2) ... Selecting previously unselected package libhttpclient-java. Preparing to unpack .../185-libhttpclient-java_4.5.7-1_all.deb ... Unpacking libhttpclient-java (4.5.7-1) ... Selecting previously unselected package libjsoup-java. Preparing to unpack .../186-libjsoup-java_1.10.2-2_all.deb ... Unpacking libjsoup-java (1.10.2-2) ... Selecting previously unselected package libwagon-http-java. Preparing to unpack .../187-libwagon-http-java_3.3.1-2_all.deb ... Unpacking libwagon-http-java (3.3.1-2) ... Selecting previously unselected package libistack-commons-java. Preparing to unpack .../188-libistack-commons-java_3.0.6-3_all.deb ... Unpacking libistack-commons-java (3.0.6-3) ... Selecting previously unselected package libcodemodel-java. Preparing to unpack .../189-libcodemodel-java_2.6+jaxb2.3.0.1-8_all.deb ... Unpacking libcodemodel-java (2.6+jaxb2.3.0.1-8) ... Selecting previously unselected package libcommons-collections3-java. Preparing to unpack .../190-libcommons-collections3-java_3.2.2-2_all.deb ... Unpacking libcommons-collections3-java (3.2.2-2) ... Selecting previously unselected package libcommons-pool-java. Preparing to unpack .../191-libcommons-pool-java_1.6-3_all.deb ... Unpacking libcommons-pool-java (1.6-3) ... Selecting previously unselected package libcommons-dbcp-java. Preparing to unpack .../192-libcommons-dbcp-java_1.4-6_all.deb ... Unpacking libcommons-dbcp-java (1.4-6) ... Selecting previously unselected package libcommons-math-java. Preparing to unpack .../193-libcommons-math-java_2.2-7_all.deb ... Unpacking libcommons-math-java (2.2-7) ... Selecting previously unselected package libdtd-parser-java. Preparing to unpack .../194-libdtd-parser-java_1.2~svn20110404-1_all.deb ... Unpacking libdtd-parser-java (1.2~svn20110404-1) ... Selecting previously unselected package libel-api-java. Preparing to unpack .../195-libel-api-java_3.0.0-2+deb10u1_all.deb ... Unpacking libel-api-java (3.0.0-2+deb10u1) ... Selecting previously unselected package libjaxb-api-java. Preparing to unpack .../196-libjaxb-api-java_2.3.1-1_all.deb ... Unpacking libjaxb-api-java (2.3.1-1) ... Selecting previously unselected package libstax-ex-java. Preparing to unpack .../197-libstax-ex-java_1.7.8-3_all.deb ... Unpacking libstax-ex-java (1.7.8-3) ... Selecting previously unselected package libstreambuffer-java. Preparing to unpack .../198-libstreambuffer-java_1.5.4-1_all.deb ... Unpacking libstreambuffer-java (1.5.4-1) ... Selecting previously unselected package librelaxng-datatype-java. Preparing to unpack .../199-librelaxng-datatype-java_1.0+ds1-3_all.deb ... Unpacking librelaxng-datatype-java (1.0+ds1-3) ... Selecting previously unselected package libxsom-java. Preparing to unpack .../200-libxsom-java_2.3.0.1-8_all.deb ... Unpacking libxsom-java (2.3.0.1-8) ... Selecting previously unselected package libfastinfoset-java. Preparing to unpack .../201-libfastinfoset-java_1.2.12-3_all.deb ... Unpacking libfastinfoset-java (1.2.12-3) ... Selecting previously unselected package libgoogle-gson-java. Preparing to unpack .../202-libgoogle-gson-java_2.8.5-3_all.deb ... Unpacking libgoogle-gson-java (2.8.5-3) ... Selecting previously unselected package libservlet-api-java. Preparing to unpack .../203-libservlet-api-java_4.0.1-2_all.deb ... Unpacking libservlet-api-java (4.0.1-2) ... Selecting previously unselected package libjsp-api-java. Preparing to unpack .../204-libjsp-api-java_2.3.4-2+deb10u1_all.deb ... Unpacking libjsp-api-java (2.3.4-2+deb10u1) ... Selecting previously unselected package libwebsocket-api-java. Preparing to unpack .../205-libwebsocket-api-java_1.1-1+deb10u1_all.deb ... Unpacking libwebsocket-api-java (1.1-1+deb10u1) ... Selecting previously unselected package libservlet3.1-java. Preparing to unpack .../206-libservlet3.1-java_1%3a4.0.1-2_all.deb ... Unpacking libservlet3.1-java (1:4.0.1-2) ... Selecting previously unselected package libhsqldb-java. Preparing to unpack .../207-libhsqldb-java_2.4.1-2_all.deb ... Unpacking libhsqldb-java (2.4.1-2) ... Selecting previously unselected package libitext5-java. Preparing to unpack .../208-libitext5-java_5.5.13-1_all.deb ... Unpacking libitext5-java (5.5.13-1) ... Selecting previously unselected package librngom-java. Preparing to unpack .../209-librngom-java_2.3.0.1-8_all.deb ... Unpacking librngom-java (2.3.0.1-8) ... Selecting previously unselected package libtxw2-java. Preparing to unpack .../210-libtxw2-java_2.3.0.1-8_all.deb ... Unpacking libtxw2-java (2.3.0.1-8) ... Selecting previously unselected package libxml-commons-resolver1.1-java. Preparing to unpack .../211-libxml-commons-resolver1.1-java_1.2-9_all.deb ... Unpacking libxml-commons-resolver1.1-java (1.2-9) ... Selecting previously unselected package libjaxb-java. Preparing to unpack .../212-libjaxb-java_2.3.0.1-8_all.deb ... Unpacking libjaxb-java (2.3.0.1-8) ... Selecting previously unselected package libjaxp1.3-java. Preparing to unpack .../213-libjaxp1.3-java_1.3.05-5_all.deb ... Unpacking libjaxp1.3-java (1.3.05-5) ... Selecting previously unselected package libjgraph-java. Preparing to unpack .../214-libjgraph-java_5.12.4.2+dfsg-5_all.deb ... Unpacking libjgraph-java (5.12.4.2+dfsg-5) ... Selecting previously unselected package libjgrapht0.8-java. Preparing to unpack .../215-libjgrapht0.8-java_0.8.3-5_all.deb ... Unpacking libjgrapht0.8-java (0.8.3-5) ... Selecting previously unselected package libnaga-java. Preparing to unpack .../216-libnaga-java_3.0+svn80-2_all.deb ... Unpacking libnaga-java (3.0+svn80-2) ... Selecting previously unselected package libjmol-java. Preparing to unpack .../217-libjmol-java_14.6.4+2016.11.05+dfsg1-4_all.deb ... Unpacking libjmol-java (14.6.4+2016.11.05+dfsg1-4) ... Selecting previously unselected package libjson-simple-java. Preparing to unpack .../218-libjson-simple-java_2.3.0-1_all.deb ... Unpacking libjson-simple-java (2.3.0-1) ... Selecting previously unselected package liblightcouch-java. Preparing to unpack .../219-liblightcouch-java_0.0.6-1_all.deb ... Unpacking liblightcouch-java (0.0.6-1) ... Selecting previously unselected package liblog4j2-java. Preparing to unpack .../220-liblog4j2-java_2.11.1-2_all.deb ... Unpacking liblog4j2-java (2.11.1-2) ... Selecting previously unselected package libnetx-java. Preparing to unpack .../221-libnetx-java_0.5-4_all.deb ... Unpacking libnetx-java (0.5-4) ... Selecting previously unselected package libvecmath-java. Preparing to unpack .../222-libvecmath-java_1.5.2-7_all.deb ... Unpacking libvecmath-java (1.5.2-7) ... Selecting previously unselected package libxmlunit-java. Preparing to unpack .../223-libxmlunit-java_1.6-1_all.deb ... Unpacking libxmlunit-java (1.6-1) ... Selecting previously unselected package rdfind. Preparing to unpack .../224-rdfind_1.4.1-1_armhf.deb ... Unpacking rdfind (1.4.1-1) ... Setting up libksba8:armhf (1.3.5-2) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up liblcms2-2:armhf (2.9-3) ... Setting up libdtd-parser-java (1.2~svn20110404-1) ... Setting up wdiff (1.2.2-2+b1) ... Setting up lsb-base (10.2019051400) ... Setting up libslf4j-java (1.7.25-3) ... Setting up libfile-which-perl (1.23-1) ... Setting up libxau6:armhf (1:1.0.8-1+b2) ... Setting up libplexus-utils2-java (3.1.1-1) ... Setting up libkeyutils1:armhf (1.6-6) ... Setting up libplexus-classworlds-java (2.6.0-1) ... Setting up mime-support (3.62) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up java-common (0.71) ... Setting up libnetx-java (0.5-4) ... Setting up libdynaloader-functions-perl (0.003-1) ... Setting up libclass-method-modifiers-perl (2.12-1) ... Setting up libaopalliance-java (20070526-6) ... Setting up libcommons-cli-java (1.4-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libvecmath-java (1.5.2-7) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libgoogle-gson-java (2.8.5-3) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up rdfind (1.4.1-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.30-1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up perl-openssl-defaults:armhf (3) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libel-api-java (3.0.0-2+deb10u1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libplexus-component-annotations-java (1.7.1-7) ... Setting up libnpth0:armhf (1.6-1) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libjson-simple-java (2.3.0-1) ... Setting up libassuan0:armhf (2.5.2-1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libplexus-cipher-java (1.7-3) ... Setting up libsnappy1v5:armhf (1.1.7-1) ... Setting up libkrb5support0:armhf (1.17-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.0-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-2) ... Setting up libasound2-data (1.1.8-1) ... Setting up patchutils (0.3.4-2) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ... Setting up junit (3.8.2-9) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libnspr4:armhf (2:4.20-1) ... Setting up gnupg-l10n (2.2.12-1+deb10u1) ... Setting up libapache-pom-java (18-1) ... Setting up libavahi-common-data:armhf (0.7-4+b1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:armhf (1.12.16-1) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libwebsocket-api-java (1.1-1+deb10u1) ... Setting up libplexus-interpolation-java (1.25-1) ... Setting up libpng16-16:armhf (1.6.36-6) ... Setting up libitext5-java (5.5.13-1) ... Setting up libxml-commons-resolver1.1-java (1.2-9) ... Setting up libxz-java (1.8-2) ... Setting up openjdk-11-doc (11.0.6+10-1~deb10u1) ... Setting up libio-html-perl (1.001-1) ... Setting up libcommons-pool-java (1.6-3) ... Setting up autopoint (0.19.8.1-9) ... Setting up libb-hooks-op-check-perl (0.22-1+b1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libpcsclite1:armhf (1.8.24-1) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libjgraph-java (5.12.4.2+dfsg-5) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (1.3-9) ... Setting up libjsp-api-java (2.3.4-2+deb10u1) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libtimedate-perl (2.3000-2+deb10u1) ... Setting up sensible-utils (0.0.12) ... Setting up libjsoup-java (1.10.2-2) ... Setting up libcommons-math-java (2.2-7) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libasound2:armhf (1.1.8-1) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.000006-1) ... Setting up libplexus-sec-dispatcher-java (1.4-4) ... Setting up libdevel-globaldestruction-perl (0.14-1) ... Setting up netbase (5.6) ... Setting up libstrictures-perl (2.000005-1) ... Setting up libsub-quote-perl (2.005001-1) ... Setting up libkrb5-3:armhf (1.17-3) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up libhttpcore-java (4.4.11-1) ... Setting up libjaxp1.3-java (1.3.05-5) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up librelaxng-datatype-java (1.0+ds1-3) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libcdi-api-java (1.2-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libsnappy-jni (1.1.7.2-1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up liburi-perl (1.76-1) ... Setting up libargs4j-java (2.33-1) ... Setting up dctrl-tools (2.24-3) ... Setting up libservlet3.1-java (1:4.0.1-2) ... Setting up libreadline7:armhf (7.0-5) ... Setting up gnupg-utils (2.2.12-1+deb10u1) ... Setting up libnaga-java (3.0+svn80-2) ... Setting up libnet-ssleay-perl (1.85-2+b1) ... Setting up pinentry-curses (1.1.0-2) ... Setting up libdom4j-java (2.1.1-2) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libwagon-provider-api-java (3.3.1-2) ... Setting up libcommons-dbcp-java (1.4-6) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libpython3.7-stdlib:armhf (3.7.3-2+deb10u1) ... Setting up libxcb1:armhf (1.13.1-2) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libjgrapht0.8-java (0.8.3-5) ... Setting up libtool (2.4.6-9) ... Setting up libhsqldb-java (2.4.1-2) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libmaven-parent-java (31-2) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:armhf (0.7-4+b1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up libnet-http-perl (6.18-1) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:armhf (2:3.42.1-1+deb10u2) ... Setting up default-jdk-doc (2:1.11-71) ... Setting up libdevel-callchecker-perl (0.008-1) ... Setting up libxmlunit-java (1.6-1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libmaven-resolver-java (1.3.1-1) ... Setting up libfreetype6:armhf (2.9.1-3+deb10u1) ... Setting up libguava-java (19.0-1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libstreambuffer-java (1.5.4-1) ... Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libcommons-lang3-java (3.8-2) ... Setting up autoconf (2.69-11) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up librngom-java (2.3.0.1-8) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libsisu-guice-java (4.2.0-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.12-1+deb10u1) ... Setting up libx11-6:armhf (2:1.6.7-1) ... Setting up libsnappy-java (1.1.7.2-1) ... Setting up libxsom-java (2.3.0.1-8) ... Setting up libcommons-codec-java (1.11-1) ... Setting up libavahi-client3:armhf (0.7-4+b1) ... Setting up libio-socket-ssl-perl (2.060-3) ... Setting up gpg (2.2.12-1+deb10u1) ... Setting up libjmol-java (14.6.4+2016.11.05+dfsg1-4) ... Setting up libpython3-stdlib:armhf (3.7.3-1) ... Setting up libhttp-message-perl (6.18-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u1) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up gettext (0.19.8.1-9) ... Setting up gpg-agent (2.2.12-1+deb10u1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libcommons-compress-java (1.18-2) ... Setting up libhttp-cookies-perl (6.04-1) ... Setting up libcommons-io-java (2.6-2) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b1) ... Setting up gpgsm (2.2.12-1+deb10u1) ... Setting up libxext6:armhf (2:1.3.3-1+b2) ... Setting up libsisu-ioc-java (2.3.0-11) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libguice-java (4.2.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up dirmngr (2.2.12-1+deb10u1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up gpg-wks-server (2.2.12-1+deb10u1) ... Setting up libcups2:armhf (2.2.10-6+deb10u3) ... Setting up libhttpclient-java (4.5.7-1) ... Setting up liblightcouch-java (0.0.6-1) ... Setting up libwagon-http-java (3.3.1-2) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfontconfig1:armhf (2.13.1-2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libplexus-io-java (3.1.1-1) ... Setting up libxi6:armhf (2:1.7.9-1) ... Setting up gpg-wks-client (2.2.12-1+deb10u1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libxtst6:armhf (2:1.2.3-1) ... Setting up libmoo-perl (2.003004-2) ... Setting up po-debconf (1.0.21) ... Setting up liblog4j2-java (2.11.1-2) ... Setting up libsisu-inject-java (0.3.3-1) ... Setting up libsisu-plexus-java (0.3.3-3) ... Setting up gnupg (2.2.12-1+deb10u1) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up libmaven3-core-java (3.6.0-1) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up default-jre-headless (2:1.11-71) ... Setting up libwww-perl (6.36-2) ... Setting up openjdk-11-jre-headless:armhf (11.0.6+10-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jdk-headless:armhf (11.0.6+10-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up dh-autoreconf (19) ... Setting up default-jdk-headless (2:1.11-71) ... Setting up devscripts (2.19.5+deb10u1) ... Setting up ant (1.10.5-2) ... Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:AffirmTrust_Networking.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Certigna.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:AddTrust_External_Root.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:EC-ACC.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Izenpe.com.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:ISRG_Root_X1.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:TrustCor_ECA-1.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Taiwan_GRCA.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:ACCVRAIZ1.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:DigiCert_Trusted_Root_G4.pem done. Setting up junit4 (4.12-8) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up ant-contrib (1.0~b3+svn177-10) ... Setting up debhelper (12.1.1) ... Setting up ant-optional (1.10.5-2) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up javahelper (0.72.9) ... Setting up libistack-commons-java (3.0.6-3) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-8) ... Setting up libtxw2-java (2.3.0.1-8) ... Setting up libjaxb-java (2.3.0.1-8) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with javahelper jh_clean debian/rules override_dh_clean make[1]: ingresso nella directory "/build/biojava4-live-4.2.12+dfsg" dh_clean rm -rf build rm -rf dist rm -rf javadoc rm -rf test rm -f biojava-*/build.xml rm -rf biojavadoc rm -rf doc find . -name "*.class" -delete rm -rf buildtest make[1]: uscita dalla directory "/build/biojava4-live-4.2.12+dfsg" debian/rules build dh build --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: ingresso nella directory "/build/biojava4-live-4.2.12+dfsg" dh_auto_configure sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml sed -e 's/BJLIB/biojava4-core/g' debian/build.xml > biojava-core/build.xml sed -e 's/BJLIB/biojava4-alignment/g' debian/build.xml > biojava-alignment/build.xml sed -e 's/BJLIB/biojava4-genome/g' debian/build.xml > biojava-genome/build.xml sed -e 's/BJLIB/biojava4-modfinder/g' debian/build.xml > biojava-modfinder/build.xml sed -e 's/BJLIB/biojava4-phylo/g' debian/build.xml > biojava-phylo/build.xml sed -e 's/BJLIB/biojava4-sequencing/g' debian/build.xml > biojava-sequencing/build.xml sed -e 's/BJLIB/biojava4-protein-disorder/g' debian/build.xml > biojava-protein-disorder/build.xml sed -e 's/BJLIB/biojava4-structure/g' debian/build.xml > biojava-structure/build.xml sed -e 's/BJLIB/biojava4-ws/g' debian/build.xml > biojava-ws/build.xml sed -e 's/BJLIB/biojava4-structure-gui/g' debian/build.xml > biojava-structure-gui/build.xml sed -e 's/BJLIB/biojava4-ontology/g' debian/build.xml > biojava-ontology/build.xml sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml make[1]: uscita dalla directory "/build/biojava4-live-4.2.12+dfsg" jh_linkjars debian/rules override_dh_auto_build make[1]: ingresso nella directory "/build/biojava4-live-4.2.12+dfsg" cd biojava-jcolorbrewer && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-jcolorbrewer/classes [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/dist [javac] /build/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 9 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-jcolorbrewer/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL Total time: 26 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 359 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-forester/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL Total time: 3 minutes 1 second cd biojava-core && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 176 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 24 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL Total time: 1 minute 22 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 8 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes [copy] Copying 2 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL Total time: 21 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 45 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 1 file to /build/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL Total time: 36 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 32 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/xml/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/convertor/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/package-info.class [copy] Copying 11 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL Total time: 33 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 30 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 1 file to /build/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL Total time: 41 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 19 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes/org/biojava/nbio/sequencing/io/fastq/package-info.class [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL Total time: 25 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 483 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 64 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL Total time: 3 minutes 11 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 136 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 49 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL Total time: 2 minutes 50 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 23 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 2 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL Total time: 1 minute 54 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 34 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 2 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL Total time: 36 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 13 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/ronn/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/data/sequence/package-info.class [copy] Copying 11 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL Total time: 1 minute 19 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 1 source file to /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL Total time: 14 seconds cd biojava-ws && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 20 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-ws/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL Total time: 23 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 46 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [copy] Copying 1 file to /build/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL Total time: 1 minute 20 seconds # make doc rm -rf biojavadoc mkdir biojavadoc cp -r biojava-*/src biojavadoc/ sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml cd biojavadoc && ant javadocs Buildfile: /build/biojava4-live-4.2.12+dfsg/biojavadoc/build.xml javadocs: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/javadoc [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/doc/biojava [javadoc] Generating Javadoc [javadoc] Debian build on Java 9+ detected: Adding the --ignore-source-errors option [javadoc] Javadoc execution [javadoc] Loading source files for package org.biojava.nbio.aaproperties... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.profeat... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.xml... [javadoc] Loading source files for package org.biojava.nbio.alignment... [javadoc] Loading source files for package org.biojava.nbio.alignment.io... [javadoc] Loading source files for package org.biojava.nbio.alignment.routines... [javadoc] Loading source files for package org.biojava.nbio.alignment.template... [javadoc] Loading source files for package org.biojava.nbio.core.alignment... [javadoc] Loading source files for package org.biojava.nbio.core.alignment.matrices... [javadoc] Loading source files for package org.biojava.nbio.core.alignment.template... [javadoc] Loading source files for package org.biojava.nbio.core.exceptions... [javadoc] Loading source files for package org.biojava.nbio.core.search.io... [javadoc] Loading source files for package org.biojava.nbio.core.search.io.blast... [javadoc] Loading source files for package org.biojava.nbio.core.sequence... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.compound... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.edits... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.features... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io.util... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.loader... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.location... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.location.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.storage... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.transcription... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.views... [javadoc] Loading source files for package org.biojava.nbio.core.util... [javadoc] Loading source files for package org.biojava.nbio.data.sequence... [javadoc] Loading source files for package org.biojava.nbio.genome... [javadoc] Loading source files for package org.biojava.nbio.genome.homology... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.cytoband... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.geneid... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.genename... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.gff... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.twobit... [javadoc] Loading source files for package org.biojava.nbio.genome.query... [javadoc] Loading source files for package org.biojava.nbio.genome.uniprot... [javadoc] Loading source files for package org.biojava.nbio.genome.util... [javadoc] Loading source files for package org.biojava.nbio.ontology... [javadoc] Loading source files for package org.biojava.nbio.ontology.io... [javadoc] Loading source files for package org.biojava.nbio.ontology.obo... [javadoc] Loading source files for package org.biojava.nbio.ontology.utils... [javadoc] Loading source files for package org.biojava.nbio.phosphosite... [javadoc] Loading source files for package org.biojava.nbio.phylo... [javadoc] Loading source files for package org.biojava.nbio.proteincomparisontool... [javadoc] Loading source files for package org.biojava.nbio.protmod... [javadoc] Loading source files for package org.biojava.nbio.protmod.io... [javadoc] Loading source files for package org.biojava.nbio.protmod.structure... [javadoc] Loading source files for package org.biojava.nbio.ronn... [javadoc] Loading source files for package org.biojava.nbio.sequencing.io.fastq... [javadoc] Loading source files for package org.biojava.nbio.structure... [javadoc] Loading source files for package org.biojava.nbio.structure.align... [javadoc] Loading source files for package org.biojava.nbio.structure.align.ce... [javadoc] Loading source files for package org.biojava.nbio.structure.align.client... [javadoc] Loading source files for package org.biojava.nbio.structure.align.events... [javadoc] Loading source files for package org.biojava.nbio.structure.align.fatcat... [javadoc] Loading source files for package org.biojava.nbio.structure.align.fatcat.calc... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.jmol... [javadoc] Loading source files for package org.biojava.nbio.structure.align.helper... [javadoc] Loading source files for package org.biojava.nbio.structure.align.model... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple.mc... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple.util... [javadoc] Loading source files for package org.biojava.nbio.structure.align.pairwise... [javadoc] Loading source files for package org.biojava.nbio.structure.align.seq... [javadoc] Loading source files for package org.biojava.nbio.structure.align.util... [javadoc] Loading source files for package org.biojava.nbio.structure.align.webstart... [javadoc] Loading source files for package org.biojava.nbio.structure.align.xml... [javadoc] Loading source files for package org.biojava.nbio.structure.asa... [javadoc] Loading source files for package org.biojava.nbio.structure.cath... [javadoc] Loading source files for package org.biojava.nbio.structure.contact... [javadoc] Loading source files for package org.biojava.nbio.structure.domain... [javadoc] Loading source files for package org.biojava.nbio.structure.domain.pdp... [javadoc] Loading source files for package org.biojava.nbio.structure.ecod... [javadoc] Loading source files for package org.biojava.nbio.structure.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.events... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.util... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.util.color... [javadoc] Loading source files for package org.biojava.nbio.structure.io... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif.chem... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif.model... [javadoc] Loading source files for package org.biojava.nbio.structure.io.sifts... [javadoc] Loading source files for package org.biojava.nbio.structure.io.util... [javadoc] Loading source files for package org.biojava.nbio.structure.jama... [javadoc] Loading source files for package org.biojava.nbio.structure.math... [javadoc] Loading source files for package org.biojava.nbio.structure.quaternary... [javadoc] Loading source files for package org.biojava.nbio.structure.quaternary.io... [javadoc] Loading source files for package org.biojava.nbio.structure.rcsb... [javadoc] Loading source files for package org.biojava.nbio.structure.scop... [javadoc] Loading source files for package org.biojava.nbio.structure.scop.server... [javadoc] Loading source files for package org.biojava.nbio.structure.secstruc... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.analysis... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.core... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.geometry... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.internal... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.misc... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.utils... [javadoc] Loading source files for package org.biojava.nbio.structure.validation... [javadoc] Loading source files for package org.biojava.nbio.structure.xtal... [javadoc] Loading source files for package org.biojava.nbio.structure.xtal.io... [javadoc] Loading source files for package org.biojava.nbio.survival.cox... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.comparators... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.matrix... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.stats... [javadoc] Loading source files for package org.biojava.nbio.survival.data... [javadoc] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure... [javadoc] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... [javadoc] Loading source files for package org.biojava.nbio.ws.alignment... [javadoc] Loading source files for package org.biojava.nbio.ws.alignment.qblast... [javadoc] Loading source files for package org.biojava.nbio.ws.hmmer... [javadoc] Loading source files for package org.forester.analysis... [javadoc] Loading source files for package org.forester.application... [javadoc] Loading source files for package org.forester.applications... [javadoc] Loading source files for package org.forester.archaeopteryx... [javadoc] Loading source files for package org.forester.archaeopteryx.phylogeny.data... [javadoc] Loading source files for package org.forester.archaeopteryx.tools... [javadoc] Loading source files for package org.forester.archaeopteryx.webservices... [javadoc] Loading source files for package org.forester.datastructures... [javadoc] Loading source files for package org.forester.development... [javadoc] Loading source files for package org.forester.evoinference... [javadoc] Loading source files for package org.forester.evoinference.distance... [javadoc] Loading source files for package org.forester.evoinference.matrix.character... [javadoc] Loading source files for package org.forester.evoinference.matrix.distance... [javadoc] Loading source files for package org.forester.evoinference.parsimony... [javadoc] Loading source files for package org.forester.evoinference.tools... [javadoc] Loading source files for package org.forester.go... [javadoc] Loading source files for package org.forester.go.etc... [javadoc] Loading source files for package org.forester.io.parsers... [javadoc] Loading source files for package org.forester.io.parsers.nexus... [javadoc] Loading source files for package org.forester.io.parsers.nhx... [javadoc] Loading source files for package org.forester.io.parsers.phyloxml... [javadoc] Loading source files for package org.forester.io.parsers.phyloxml.data... [javadoc] Loading source files for package org.forester.io.parsers.tol... [javadoc] Loading source files for package org.forester.io.parsers.util... [javadoc] Loading source files for package org.forester.io.writers... [javadoc] Loading source files for package org.forester.msa... [javadoc] Loading source files for package org.forester.msa_compactor... [javadoc] Loading source files for package org.forester.pccx... [javadoc] Loading source files for package org.forester.phylogeny... [javadoc] Loading source files for package org.forester.phylogeny.data... [javadoc] Loading source files for package org.forester.phylogeny.factories... [javadoc] Loading source files for package org.forester.phylogeny.iterators... [javadoc] Loading source files for package org.forester.protein... [javadoc] Loading source files for package org.forester.rio... [javadoc] Loading source files for package org.forester.sdi... [javadoc] Loading source files for package org.forester.sequence... [javadoc] Loading source files for package org.forester.species... [javadoc] Loading source files for package org.forester.surfacing... [javadoc] Loading source files for package org.forester.test... [javadoc] Loading source files for package org.forester.test.examples... [javadoc] Loading source files for package org.forester.tools... [javadoc] Loading source files for package org.forester.util... [javadoc] Loading source files for package org.forester.ws.hmmer... [javadoc] Loading source files for package org.forester.ws.seqdb... [javadoc] Loading source files for package org.forester.ws.wabi... [javadoc] Loading source files for package org.jcolorbrewer... [javadoc] Loading source files for package org.jcolorbrewer.ui... [javadoc] Constructing Javadoc information... [javadoc] javadoc: error - Error fetching URL: http://java.sun.com/j2se/1.6.0/docs/api/ [javadoc] Standard Doclet version 11.0.6 [javadoc] Building tree for all the packages and classes... [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag < [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag > [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag < [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag > [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:38: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:39: warning - Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java:44: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java:163: warning - @param argument "dbReference" is not a parameter name. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning - invalid usage of tag < [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning - @param argument "cutsPerSection" is not a parameter name. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning - @param argument "cutsPerSection" is not a parameter name. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning - invalid usage of tag < [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:105: warning - invalid usage of tag > [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:130: warning - invalid usage of tag > [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning - Tag @link: reference not found: Aligner [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning - invalid usage of tag < [javadoc] Building index for all the packages and classes... [javadoc] Building index for all classes... [javadoc] Building index for all classes... [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/help-doc.html... [javadoc] 1 error [javadoc] 100 warnings BUILD SUCCESSFUL Total time: 6 minutes 10 seconds # rm -rf biojavadoc make[1]: uscita dalla directory "/build/biojava4-live-4.2.12+dfsg" debian/rules override_dh_auto_test make[1]: ingresso nella directory "/build/biojava4-live-4.2.12+dfsg" echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' * The following test is ignored since under certain circumstances it might fail * echo '* Please check the result! *' * Please check the result! * echo '* More information can be found in the Debian BTS at *' * More information can be found in the Debian BTS at * echo '* https://bugs.debian.org/843712 *' * https://bugs.debian.org/843712 * echo '*********************************************************************************' ********************************************************************************* cd biojava-core && (ant test || true) Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 30 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 21 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [copy] Copying 176 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.575 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.575 sec [junit] [junit] Testcase: testGetIndexOf took 0.224 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.003 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.002 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.002 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetNumGaps took 0.003 sec [junit] Testcase: testGetStart took 0.001 sec [junit] Testcase: testGetSequenceIndexAt took 0.002 sec [junit] Testcase: testGetAccession took 0.001 sec [junit] Testcase: testToString took 0.009 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0.002 sec [junit] Testcase: testCountCompounds took 0.004 sec [junit] Testcase: testGetAlignmentIndexAt took 0.002 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.002 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.002 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.009 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.011 sec [junit] Testcase: testGetOriginalSequence took 0.002 sec [junit] Testcase: testGetCompoundAt took 0.002 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testIsCircular took 0.001 sec [junit] Testcase: testGetEnd took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceLocal took 0.002 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0.001 sec [junit] Testcase: testGetOverlapCount took 0.001 sec [junit] Testcase: testGetCompoundSet took 0.001 sec [junit] Testcase: testGetLocationInAlignment took 0.006 sec [junit] Testcase: testIterator took 0.002 sec [junit] Testcase: testGetSequenceAsString took 0.003 sec [junit] Testcase: testGetLastIndexOf took 0.002 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.011 sec [junit] Running org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.1 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.1 sec [junit] [junit] Testcase: testGetIndexOf took 0.419 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.005 sec [junit] Testcase: testGetAlignedSequenceInt took 0.008 sec [junit] Testcase: testToStringInt took 0.055 sec [junit] Testcase: testToString took 0.005 sec [junit] Testcase: testToStringFormatted took 0.18 sec [junit] Testcase: testSimpleProfile took 0.002 sec [junit] Testcase: testGetSize took 0.002 sec [junit] Testcase: testGetAlignedSequenceS took 0.003 sec [junit] Testcase: testGetAlignedSequences took 0.003 sec [junit] Testcase: testGetOriginalSequences took 0.002 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0.002 sec [junit] Testcase: testGetAlignedSequencesSArray took 0.004 sec [junit] Testcase: testGetIndicesAt took 0.012 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.003 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.008 sec [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.003 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.002 sec [junit] Testcase: testIsCircular took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.002 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.002 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.002 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.002 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.002 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.002 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.034 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.002 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.002 sec [junit] Testcase: testGetCompoundSet took 0.001 sec [junit] Testcase: testGetCompoundsAt took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.002 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.002 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec [junit] Testcase: testIterator took 0.002 sec [junit] Testcase: testGetLastIndexOf took 0.005 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.003 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.002 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.002 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.002 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.003 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.002 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.002 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0.002 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.63 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.63 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.336 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.002 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInTargetAt took 0.002 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.002 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.002 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.002 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.002 sec [junit] Testcase: testGetCompoundInQueryAt took 0.002 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.002 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.007 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0.002 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.002 sec [junit] Testcase: testGetNumIdenticals took 0.003 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0.002 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.002 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetCompoundInTargetAt took 0.002 sec [junit] Testcase: testGetIndexInQueryAt took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.002 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumSimilars took 0.009 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.002 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.002 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.602 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.602 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetAlignment took 0.305 sec [junit] Testcase: testHashCode took 0.001 sec [junit] Testcase: testEquals took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 2.091 sec [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 2.091 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] Jun 11, 2020 6:23:58 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Jun 11, 2020 6:23:59 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testConstructorWithEvalueHspFilter took 1.151 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov [junit] junit.framework.AssertionFailedError: test failed: [junit] www.ncbi.nlm.nih.gov [junit] at org.biojava.nbio.core.search.io.SearchIOTest.testConstructorWithEvalueHspFilter(SearchIOTest.java:110) [junit] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [junit] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [junit] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [junit] [junit] Testcase: testConstructorWithFactoryGuess took 0.728 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0.029 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov [junit] junit.framework.AssertionFailedError: test failed: [junit] www.ncbi.nlm.nih.gov [junit] at org.biojava.nbio.core.search.io.SearchIOTest.testConstructorWithoutFactoryGuess(SearchIOTest.java:92) [junit] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [junit] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [junit] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [junit] BUILD FAILED /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:123: Test org.biojava.nbio.core.search.io.SearchIOTest failed Total time: 1 minute 4 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 22 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 10 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 45 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.642 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.642 sec [junit] [junit] Testcase: testGetQuery took 0.319 sec [junit] Testcase: testGetScore took 0.15 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.003 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.005 sec [junit] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.665 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.665 sec [junit] [junit] Testcase: testGetQuery took 0.316 sec [junit] Testcase: testGetScore took 0.156 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.009 sec [junit] Testcase: testGetMinScore took 0.003 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.003 sec [junit] Testcase: testGetTarget took 0.003 sec [junit] Testcase: testGetMaxScore took 0.013 sec [junit] Running org.biojava.nbio.alignment.GuideTreeTest [junit] Testsuite: org.biojava.nbio.alignment.GuideTreeTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.183 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.183 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGuideTree took 0.775 sec [junit] Testcase: testToString took 0.019 sec [junit] Testcase: testGetScoreMatrix took 0.028 sec [junit] Testcase: testGetRoot took 0.131 sec [junit] Testcase: testGetSequences took 0.019 sec [junit] Testcase: testGetDistanceMatrix took 0.016 sec [junit] Testcase: testGetAllPairsScores took 0.017 sec [junit] Testcase: testIterator took 0.014 sec [junit] Running org.biojava.nbio.alignment.LocalAlignmentTest [junit] Testsuite: org.biojava.nbio.alignment.LocalAlignmentTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.718 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.718 sec [junit] [junit] Testcase: shouldAllowZeroLengthMatches took 0.571 sec [junit] Running org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.53 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.53 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.308 sec [junit] Testcase: testGetGapPenalty took 0.001 sec [junit] Testcase: testGetComputationTime took 0.148 sec [junit] Testcase: should_align_middle_anchor took 0.167 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.004 sec [junit] Testcase: testNeedlemanWunsch took 0.005 sec [junit] Testcase: should_align_all_anchored took 0.005 sec [junit] Testcase: testGetScoreMatrix took 0.004 sec [junit] Testcase: testGetPair took 0.006 sec [junit] Testcase: should_align_multiple_anchors took 0.005 sec [junit] Testcase: testAnchoredDNAAlignment took 0.019 sec [junit] Testcase: testGetProfile took 0.006 sec [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: should_align_ending_anchor took 0.004 sec [junit] Testcase: testIsStoringScoreMatrix took 0.007 sec [junit] Testcase: testComplex took 0.134 sec [junit] Testcase: testGetScoreMatrixAsString took 0.079 sec [junit] Testcase: should_align_starting_anchor took 0.003 sec [junit] Testcase: anchors_should_not_change_score took 0.003 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Testcase: testIntOverflowBug took 1.411 sec [junit] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleGapPenaltyTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.175 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.175 sec [junit] [junit] Testcase: testOpenPenalty took 0.015 sec [junit] Testcase: testType took 0 sec [junit] Testcase: testExtensionPenalty took 0 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0.001 sec [junit] Testcase: testSimpleGapPenalty took 0.001 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.669 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.669 sec [junit] [junit] Testcase: testGetQuery took 0.487 sec [junit] Testcase: testGetTarget took 0.006 sec [junit] Testcase: testSimpleProfilePair took 0.024 sec [junit] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.082 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.082 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.494 sec [junit] Testcase: testGetGapPenalty took 0.026 sec [junit] Testcase: testGetComputationTime took 0.024 sec [junit] Testcase: testGetQuery took 0.021 sec [junit] Testcase: testGetScore took 0.023 sec [junit] Testcase: testGetScoreMatrix took 0.024 sec [junit] Testcase: testGetPair took 0.032 sec [junit] Testcase: testGetProfile took 0.016 sec [junit] Testcase: testGetMinScore took 0.011 sec [junit] Testcase: testIsStoringScoreMatrix took 0.011 sec [junit] Testcase: testGetScoreMatrixAsString took 0.145 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.011 sec [junit] Testcase: testSimpleProfileProfileAligner took 0.014 sec [junit] Testcase: testGetTarget took 0.011 sec [junit] Testcase: testGetMaxScore took 0.014 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.677 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.677 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.03 sec [junit] Testcase: testSetDescription took 0.092 sec [junit] Testcase: testToString took 0.164 sec [junit] Testcase: testCaseEquivalence took 0.004 sec [junit] Testcase: test took 0.063 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.074 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.014 sec [junit] Testcase: testSetName took 0.046 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.015 sec [junit] Running org.biojava.nbio.alignment.SmithWatermanTest [junit] Testsuite: org.biojava.nbio.alignment.SmithWatermanTest [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.943 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.943 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.313 sec [junit] Testcase: testGetGapPenalty took 0.003 sec [junit] Testcase: testGetComputationTime took 0.155 sec [junit] Testcase: testGetQuery took 0.004 sec [junit] Testcase: testGetScore took 0.015 sec [junit] Testcase: testGetScoreMatrix took 0.015 sec [junit] Testcase: testGetPair took 0.032 sec [junit] Testcase: testSmithWaterman took 0.009 sec [junit] Testcase: testGetProfile took 0.013 sec [junit] Testcase: testGetMinScore took 0.008 sec [junit] Testcase: testIsStoringScoreMatrix took 0.003 sec [junit] Testcase: testGetScoreMatrixAsString took 0.186 sec [junit] Testcase: testSetStoringScoreMatrix took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.004 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.225 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.225 sec [junit] [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.02 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.012 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0.001 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0.001 sec [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0.001 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0.001 sec [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.86 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.86 sec [junit] [junit] Testcase: testGetComputationTime took 0.488 sec [junit] Testcase: testGuanUberbacher took 0.004 sec [junit] Testcase: testGetScore took 0.004 sec [junit] Testcase: testGetPair took 0.025 sec [junit] Testcase: testGetProfile took 0.006 sec [junit] Testcase: testGetMinScore took 0.003 sec [junit] Testcase: should_align_shorter_target took 0.149 sec [junit] Testcase: should_align_multiple_cuts took 0.005 sec [junit] Testcase: testGetMaxScore took 0.004 sec [junit] Testcase: should_align_shorter_query took 0.003 sec BUILD SUCCESSFUL Total time: 1 minute 10 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 9 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 7 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [copy] Copying 32 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.095 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.095 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 [junit] SAOV_0094,45884.0164,57760.0,57760.0,8.5193 [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testAdvancedXMLExample took 3.46 sec [junit] Testcase: testExample1 took 0.179 sec [junit] Testcase: testExample2 took 0.076 sec [junit] Testcase: testExample3 took 0.036 sec [junit] Testcase: testExample1WithCSV took 0.149 sec [junit] Testcase: testWithCases took 0.03 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.486 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.486 sec [junit] [junit] Testcase: shortExample1 took 0.171 sec [junit] Testcase: shortExample2 took 2.579 sec [junit] Testcase: shortExample3 took 0.394 sec [junit] Testcase: shortExample4 took 0.011 sec [junit] Testcase: shortExample5 took 0.063 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.175 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.175 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testAdvancedXMLExample took 3.278 sec [junit] Testcase: testExample1 took 0.269 sec [junit] Testcase: testExample2 took 0.132 sec [junit] Testcase: testExample3 took 0.099 sec [junit] Testcase: testExample1WithCSV took 0.137 sec [junit] Testcase: testWithCases took 0.097 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.916 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.916 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Molecular weight is 0.0, can't divide by 0: setting absorbance to 0.0 [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Molecular weight is 0.0, can't divide by 0: setting absorbance to 0.0 [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Valid length of sequence is 0, can't divide by 0 to calculate average hydropathy: setting average hydropathy to 0 [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'Z are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Valid length of sequence is 0, can't divide by 0 to calculate instability index: setting instability index value to 0.0 [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testAbsorbance took 0.202 sec [junit] Testcase: testMolecularWeightXMLSingleFile took 2.948 sec [junit] Testcase: testEnrichment took 0.113 sec [junit] Testcase: testApliphaticIndex took 0.012 sec [junit] Testcase: testMolecularWeightXMLNull took 0.029 sec [junit] Testcase: testApliphaticIndexNull took 0.001 sec [junit] Testcase: testIsoelectricPointExpasy took 0.174 sec [junit] Testcase: testAbsorbanceNull took 0 sec [junit] Testcase: testIsoelectricPointNull took 0.001 sec [junit] Testcase: testAverageHydropathy took 0.005 sec [junit] Testcase: testExtinctionCoefficient took 0.009 sec [junit] Testcase: testAAComposition took 0.007 sec [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.394 sec [junit] Testcase: testMolecularWeight took 0.006 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.041 sec [junit] Testcase: testNetChargeNull took 0.001 sec [junit] Testcase: testExtinctionCoefficientNull took 0.001 sec [junit] Testcase: testNetCharge took 0.904 sec [junit] Testcase: testEnrichmentNull took 0.003 sec [junit] Testcase: testInstabilityIndexNull took 0.001 sec [junit] Testcase: testAverageHydropathyNull took 0.001 sec [junit] Testcase: testMolecularWeightXML took 0.744 sec [junit] Testcase: testInstabilityIndex took 0.003 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 sec [junit] [junit] Testcase: testFake took 0.007 sec [junit] Running org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.264 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.264 sec [junit] [junit] Testcase: testFakeTest took 0.006 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.312 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.312 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'J are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: generateSchema took 2.369 sec [junit] Testcase: readWithIDXml took 0.728 sec [junit] Testcase: readMinXml took 0.296 sec [junit] Testcase: readAdvancedXml took 0.176 sec [junit] Testcase: generateXml took 0.143 sec [junit] Testcase: readXml took 0.437 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.807 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.807 sec [junit] [junit] Testcase: generateSchema took 2.337 sec [junit] Testcase: generateXml took 0.372 sec [junit] Testcase: readXml took 0.835 sec [junit] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.264 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.264 sec [junit] [junit] Testcase: testFake took 0.006 sec BUILD SUCCESSFUL Total time: 1 minute 17 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 2 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 2 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 8 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes test: [echo] Using java version 11.0.6 BUILD SUCCESSFUL Total time: 15 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 14 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 74 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 19 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.856 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.856 sec [junit] [junit] Testcase: testConvert took 0.78 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec [junit] [junit] Testcase: testBuildAppendSequence took 0.03 sec [junit] Testcase: testBuildNullDescription took 0.001 sec [junit] Testcase: testBuildAppendQuality took 0.001 sec [junit] Testcase: testBuild took 0.005 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0.001 sec [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0.001 sec [junit] Testcase: testBuildNullSequence took 0 sec [junit] Testcase: testBuildMissingDescription took 0.001 sec [junit] Testcase: testBuildNullVariant took 0.001 sec [junit] Testcase: testBuildDefault took 0 sec [junit] Testcase: testBuildMissingSequence took 0 sec [junit] Testcase: testBuildNullQuality took 0.001 sec [junit] Testcase: testBuildMultiple took 0.002 sec [junit] Testcase: testConstructor took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 sec [junit] [junit] Testcase: testImmutable took 0.013 sec [junit] Testcase: testBuilder took 0.017 sec [junit] Testcase: testVariant took 0.001 sec [junit] Testcase: testQuality took 0.013 sec [junit] Testcase: testHashCode took 0.001 sec [junit] Testcase: testEquals took 0.001 sec [junit] Testcase: testDescription took 0 sec [junit] Testcase: testConstructor took 0.001 sec [junit] Testcase: testSequence took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.539 sec [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.539 sec [junit] [junit] Testcase: testErrorProbabilitiesNullFastq took 0.014 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.007 sec [junit] Testcase: testConvertNullVariant took 0.001 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.004 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.324 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0.001 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0.001 sec [junit] Testcase: testCreateQualityScores took 0.004 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec [junit] Testcase: testConvertQualitiesNullFastq took 0.001 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0.001 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0.001 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0.001 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.005 sec [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0.001 sec [junit] Testcase: testQualityScores took 0.029 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0.001 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0.001 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec [junit] Testcase: testCreateDNASequence took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0.002 sec [junit] Testcase: testCreateDNASequenceWithQualityScores took 0.001 sec [junit] Testcase: testQualityScoresIntArray took 0.001 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testToList took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0.001 sec [junit] Testcase: testErrorProbabilities took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 sec [junit] [junit] Testcase: testParseFastqVariant took 0.021 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0.002 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0.001 sec [junit] Testcase: testIsSanger took 0.013 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0.001 sec [junit] Testcase: testIsSolexa took 0 sec [junit] Testcase: testIsIllumina took 0 sec [junit] Testcase: testDescription took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.899 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.899 sec [junit] [junit] Testcase: testFullRangeAsIllumina took 0.218 sec [junit] Testcase: testWrappingAsIllumina took 0.022 sec [junit] Testcase: testValidateDescription took 0.046 sec [junit] Testcase: testValidateRepeatDescription took 0.018 sec [junit] Testcase: testMiscDnaAsIllumina took 0.017 sec [junit] Testcase: testMiscRnaAsIllumina took 0.017 sec [junit] Testcase: testLongReadsAsIllumina took 0.029 sec [junit] Testcase: testParseNullReadable took 0.004 sec [junit] Testcase: testReadRoundTripSingleFile took 0.157 sec [junit] Testcase: testReadEmptyFile took 0.002 sec [junit] Testcase: testErrorExamples took 0.206 sec [junit] Testcase: testParse took 0.004 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.009 sec [junit] Testcase: testReadEmptyInputStream took 0.008 sec [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0.002 sec [junit] Testcase: testMultipleWrappedQuality took 0.008 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.003 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testReadEmptyURL took 0.004 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.004 sec [junit] Testcase: testWrappedQuality took 0.008 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.306 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.306 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.047 sec [junit] Testcase: testAppendVararg took 0.002 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testWriteOutputStreamVararg took 0.015 sec [junit] Testcase: testWriteFileIterable took 0.139 sec [junit] Testcase: testWriteOutputStreamIterable took 0.003 sec [junit] Testcase: testAppendIterable took 0.002 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testWriteFileVararg took 0.011 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.97 sec [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.97 sec [junit] [junit] Testcase: testMiscRnaAsSanger took 0.215 sec [junit] Testcase: testFullRangeAsSanger took 0.022 sec [junit] Testcase: testWrappingOriginal took 0.02 sec [junit] Testcase: testLongReadsOriginal took 0.04 sec [junit] Testcase: testMiscDnaOriginal took 0.016 sec [junit] Testcase: testMiscRnaOriginal took 0.016 sec [junit] Testcase: testValidateDescription took 0.048 sec [junit] Testcase: testValidateRepeatDescription took 0.016 sec [junit] Testcase: testFullRangeOriginal took 0.017 sec [junit] Testcase: testWrappingAsSanger took 0.017 sec [junit] Testcase: testLongReadsAsSanger took 0.022 sec [junit] Testcase: testMiscDnaAsSanger took 0.011 sec [junit] Testcase: testParseNullReadable took 0.005 sec [junit] Testcase: testReadRoundTripSingleFile took 0.15 sec [junit] Testcase: testReadEmptyFile took 0.001 sec [junit] Testcase: testErrorExamples took 0.188 sec [junit] Testcase: testParse took 0.005 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.008 sec [junit] Testcase: testReadEmptyInputStream took 0.007 sec [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0.002 sec [junit] Testcase: testMultipleWrappedQuality took 0.009 sec [junit] Testcase: testCreateFastqReader took 0.001 sec [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.004 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.005 sec [junit] Testcase: testWrappedQuality took 0.007 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.307 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.307 sec [junit] [junit] Testcase: testConvertNotSangerVariant took 0.048 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.015 sec [junit] Testcase: testWriteFileIterable took 0.139 sec [junit] Testcase: testWriteOutputStreamIterable took 0.003 sec [junit] Testcase: testAppendIterable took 0.002 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.011 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.9 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.9 sec [junit] [junit] Testcase: testMiscRnaAsSolexa took 0.217 sec [junit] Testcase: testFullRangeAsSolexa took 0.023 sec [junit] Testcase: testValidateDescription took 0.049 sec [junit] Testcase: testValidateRepeatDescription took 0.02 sec [junit] Testcase: testWrappingAsSolexa took 0.017 sec [junit] Testcase: testLongReadsAsSolexa took 0.033 sec [junit] Testcase: testMiscDnaAsSolexa took 0.012 sec [junit] Testcase: testParseNullReadable took 0.004 sec [junit] Testcase: testReadRoundTripSingleFile took 0.157 sec [junit] Testcase: testReadEmptyFile took 0.002 sec [junit] Testcase: testErrorExamples took 0.205 sec [junit] Testcase: testParse took 0.004 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.009 sec [junit] Testcase: testReadEmptyInputStream took 0.008 sec [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0.002 sec [junit] Testcase: testMultipleWrappedQuality took 0.009 sec [junit] Testcase: testCreateFastqReader took 0.001 sec [junit] Testcase: testReadURL took 0.002 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testReadEmptyURL took 0.003 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.004 sec [junit] Testcase: testWrappedQuality took 0.008 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.309 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.309 sec [junit] [junit] Testcase: testConvertNotSolexaVariant took 0.049 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.014 sec [junit] Testcase: testWriteFileIterable took 0.14 sec [junit] Testcase: testWriteOutputStreamIterable took 0.003 sec [junit] Testcase: testAppendIterable took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testWriteFileVararg took 0.012 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 sec [junit] [junit] Testcase: testStreamNullVariant took 0.015 sec [junit] Testcase: testStreamNullListener took 0.016 sec [junit] Testcase: testStreamNullReadable took 0.004 sec BUILD SUCCESSFUL Total time: 57 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure #cd biojava-protein-disorder && ant test # Requires remote access and tmp directory write access #cd biojava-structure && ant test cd biojava-structure-gui && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 5 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/src/test/resources does not exist. [copy] Copying 141 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec [junit] [junit] Testcase: testMe took 0.005 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec [junit] [junit] Testcase: testSomeMethod took 0.005 sec [junit] Running org.biojava.nbio.structure.gui.StructureViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.StructureViewerTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec [junit] [junit] Testcase: testGetColor took 0.015 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec [junit] Testcase: testGetSelection took 0.012 sec [junit] Testcase: testRepaint took 0.001 sec [junit] Testcase: testSetSelection took 0.001 sec [junit] Testcase: testSetZoom took 0.001 sec [junit] Testcase: testSetColor took 0.001 sec [junit] Testcase: testSetStyle took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec [junit] [junit] Testcase: testStructureLoad took 0.004 sec BUILD SUCCESSFUL Total time: 26 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 2 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 5 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 36 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes test: [echo] Using java version 11.0.6 BUILD SUCCESSFUL Total time: 14 seconds make[1]: uscita dalla directory "/build/biojava4-live-4.2.12+dfsg" create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with javahelper dh_testroot dh_prep dh_install debian/rules override_jh_installjavadoc make[1]: ingresso nella directory "/build/biojava4-live-4.2.12+dfsg" jh_installjavadoc rdfind -makesymlinks true -followsymlinks true \ /usr/share/doc/openjdk-11-jre-headless \ debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java/ Now scanning "/usr/share/doc/openjdk-11-jre-headless", found 10334 files. Now scanning "debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java", found 1874 files. Now have 12208 files in total. Removed 0 files due to nonunique device and inode. Total size is 323318469 bytes or 308 MiB Removed 7242 files due to unique sizes from list.4966 files left. Now eliminating candidates based on first bytes:removed 804 files from list.4162 files left. Now eliminating candidates based on last bytes:removed 19 files from list.4143 files left. Now eliminating candidates based on sha1 checksum:removed 4103 files from list.40 files left. It seems like you have 40 files that are not unique Totally, 1 MiB can be reduced. Now making results file results.txt Now making symbolic links. creating Failed moving /usr/share/doc/openjdk-11-jre-headless/api/jquery/external/jquery/jquery.js to a temporary file Failed to make symlink /usr/share/doc/openjdk-11-jre-headless/api/jquery/external/jquery/jquery.js to /usr/share/doc/openjdk-11-jre-headless/api/jquery/jquery-3.3.1.js Making 20 links. make[1]: uscita dalla directory "/build/biojava4-live-4.2.12+dfsg" dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: generazione del pacchetto "libbiojava4-java-doc" in "../libbiojava4-java-doc_4.2.12+dfsg-2_all.deb". dpkg-deb: generazione del pacchetto "libbiojava4-java" in "../libbiojava4-java_4.2.12+dfsg-2_all.deb". dpkg-deb: generazione del pacchetto "libbiojava4.0-java" in "../libbiojava4.0-java_4.2.12+dfsg-2_all.deb". dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava4-live_4.2.12+dfsg-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/3549/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3549/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/3549 and its subdirectories I: Current time: Thu Jun 11 06:30:59 +14 2020 I: pbuilder-time-stamp: 1591806659