I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 6 19:24:44 -12 2021 I: pbuilder-time-stamp: 1617780284 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 Fri Jan 18 07:48:29 2019 -12 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/48295/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='7b6ff1c9f2fd4bc4abc9b6ef742e550c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='48295' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.k2fs6N0dHF/pbuilderrc_sF3Y --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.k2fs6N0dHF/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Mar 20 20:25 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/48295/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 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 ... 19195 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 362 MB of archives. After unpacking 900 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u5 [1539 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 netbase all 5.6 [19.4 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u5 [844 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u1 [757 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.9.1+1-1~deb10u2 [37.7 MB] Get: 65 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 ant all 1.10.5-2 [2082 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 ant-contrib all 1.0~b3+svn177-10 [262 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 ant-optional all 1.10.5-2 [379 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 dctrl-tools amd64 2.24-3 [103 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 openjdk-11-doc all 11.0.9.1+1-1~deb10u2 [13.5 MB] Get: 93 http://deb.debian.org/debian buster/main amd64 default-jdk-doc amd64 2:1.11-71 [10.9 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 openjdk-11-jdk-headless amd64 11.0.9.1+1-1~deb10u2 [229 MB] Get: 95 http://deb.debian.org/debian buster/main amd64 default-jdk-headless amd64 2:1.11-71 [1104 B] Get: 96 http://deb.debian.org/debian buster/main amd64 libassuan0 amd64 2.5.2-1 [49.4 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 gpgconf amd64 2.2.12-1+deb10u1 [510 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libksba8 amd64 1.3.5-2 [99.7 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libnpth0 amd64 1.6-1 [18.4 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 dirmngr amd64 2.2.12-1+deb10u1 [712 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 gnupg-l10n all 2.2.12-1+deb10u1 [1010 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 gnupg-utils amd64 2.2.12-1+deb10u1 [861 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 gpg amd64 2.2.12-1+deb10u1 [865 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 pinentry-curses amd64 1.1.0-2 [64.5 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 gpg-agent amd64 2.2.12-1+deb10u1 [617 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 gpg-wks-client amd64 2.2.12-1+deb10u1 [485 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 gpg-wks-server amd64 2.2.12-1+deb10u1 [478 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 gpgsm amd64 2.2.12-1+deb10u1 [604 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 gnupg all 2.2.12-1+deb10u1 [715 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get: 120 http://deb.debian.org/debian buster/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get: 121 http://deb.debian.org/debian buster/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b1 [11.4 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libdevel-callchecker-perl amd64 0.008-1 [15.7 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libparams-classify-perl amd64 0.015-1+b1 [25.5 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 librole-tiny-perl all 2.000006-1 [19.4 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 libstrictures-perl all 2.000005-1 [18.3 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libsub-quote-perl all 2.005001-1 [17.9 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 libmoo-perl all 2.003004-2 [57.4 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 libtimedate-perl all 2.3000-2+deb10u1 [38.1 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get: 138 http://deb.debian.org/debian buster/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get: 141 http://deb.debian.org/debian buster/main amd64 libhttp-message-perl all 6.18-1 [77.8 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 libhttp-cookies-perl all 6.04-1 [17.8 kB] Get: 143 http://deb.debian.org/debian buster/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get: 145 http://deb.debian.org/debian buster/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 libnet-http-perl all 6.18-1 [24.5 kB] Get: 148 http://deb.debian.org/debian buster/main amd64 liblwp-protocol-https-perl all 6.07-2 [9242 B] Get: 149 http://deb.debian.org/debian buster/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 150 http://deb.debian.org/debian buster/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 151 http://deb.debian.org/debian buster/main amd64 libwww-perl all 6.36-2 [188 kB] Get: 152 http://deb.debian.org/debian buster/main amd64 patchutils amd64 0.3.4-2 [90.4 kB] Get: 153 http://deb.debian.org/debian buster/main amd64 wdiff amd64 1.2.2-2+b1 [122 kB] Get: 154 http://deb.debian.org/debian buster/main amd64 devscripts amd64 2.19.5+deb10u1 [1046 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 javahelper all 0.72.9 [96.4 kB] Get: 156 http://deb.debian.org/debian buster/main amd64 junit all 3.8.2-9 [110 kB] Get: 157 http://deb.debian.org/debian buster/main amd64 libhamcrest-java all 1.3-9 [388 kB] Get: 158 http://deb.debian.org/debian buster/main amd64 junit4 all 4.12-8 [292 kB] Get: 159 http://deb.debian.org/debian buster/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 160 http://deb.debian.org/debian buster/main amd64 libaopalliance-java all 20070526-6 [9048 B] Get: 161 http://deb.debian.org/debian buster/main amd64 libapache-pom-java all 18-1 [4676 B] Get: 162 http://deb.debian.org/debian buster/main amd64 libargs4j-java all 2.33-1 [139 kB] Get: 163 http://deb.debian.org/debian buster/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 164 http://deb.debian.org/debian buster/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 165 http://deb.debian.org/debian buster/main amd64 libcdi-api-java all 1.2-2 [54.5 kB] Get: 166 http://deb.debian.org/debian buster/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 167 http://deb.debian.org/debian buster/main amd64 libdom4j-java all 2.1.1-2 [310 kB] Get: 168 http://deb.debian.org/debian buster/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get: 169 http://deb.debian.org/debian buster/main amd64 libcommons-io-java all 2.6-2 [213 kB] Get: 170 http://deb.debian.org/debian buster/main amd64 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 171 http://deb.debian.org/debian buster/main amd64 libcommons-cli-java all 1.4-1 [55.2 kB] Get: 172 http://deb.debian.org/debian buster/main amd64 libcommons-lang3-java all 3.8-2 [478 kB] Get: 173 http://deb.debian.org/debian buster/main amd64 libgeronimo-annotation-1.3-spec-java all 1.0-1 [10.6 kB] Get: 174 http://deb.debian.org/debian buster/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 175 http://deb.debian.org/debian buster/main amd64 libguava-java all 19.0-1 [2028 kB] Get: 176 http://deb.debian.org/debian buster/main amd64 libguice-java all 4.2.1-1 [962 kB] Get: 177 http://deb.debian.org/debian buster/main amd64 libmaven-parent-java all 31-2 [5100 B] Get: 178 http://deb.debian.org/debian buster/main amd64 libplexus-utils2-java all 3.1.1-1 [249 kB] Get: 179 http://deb.debian.org/debian buster/main amd64 libwagon-provider-api-java all 3.3.1-2 [50.1 kB] Get: 180 http://deb.debian.org/debian buster/main amd64 libmaven-resolver-java all 1.3.1-1 [549 kB] Get: 181 http://deb.debian.org/debian buster/main amd64 libplexus-cipher-java all 1.7-3 [15.0 kB] Get: 182 http://deb.debian.org/debian buster/main amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 183 http://deb.debian.org/debian buster/main amd64 libplexus-component-annotations-java all 1.7.1-7 [7536 B] Get: 184 http://deb.debian.org/debian buster/main amd64 libplexus-interpolation-java all 1.25-1 [76.8 kB] Get: 185 http://deb.debian.org/debian buster/main amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 186 http://deb.debian.org/debian buster/main amd64 libslf4j-java all 1.7.25-3 [143 kB] Get: 187 http://deb.debian.org/debian buster/main amd64 libsisu-inject-java all 0.3.3-1 [347 kB] Get: 188 http://deb.debian.org/debian buster/main amd64 libsisu-plexus-java all 0.3.3-3 [182 kB] Get: 189 http://deb.debian.org/debian buster/main amd64 libmaven3-core-java all 3.6.0-1 [1465 kB] Get: 190 http://deb.debian.org/debian buster/main amd64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 191 http://deb.debian.org/debian buster/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 192 http://deb.debian.org/debian buster/main amd64 libcommons-compress-java all 1.18-2+deb10u1 [531 kB] Get: 193 http://deb.debian.org/debian buster/main amd64 libplexus-io-java all 3.1.1-1 [64.6 kB] Get: 194 http://deb.debian.org/debian buster/main amd64 libsnappy1v5 amd64 1.1.7-1 [17.0 kB] Get: 195 http://deb.debian.org/debian buster/main amd64 libsnappy-jni amd64 1.1.7.2-1 [7148 B] Get: 196 http://deb.debian.org/debian buster/main amd64 libsnappy-java all 1.1.7.2-1 [73.7 kB] Get: 197 http://deb.debian.org/debian buster/main amd64 libxz-java all 1.8-2 [141 kB] Get: 198 http://deb.debian.org/debian buster/main amd64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 199 http://deb.debian.org/debian buster/main amd64 libsisu-guice-java all 4.2.0-1 [785 kB] Get: 200 http://deb.debian.org/debian buster/main amd64 libsisu-ioc-java all 2.3.0-11 [492 kB] Get: 201 http://deb.debian.org/debian buster/main amd64 libhttpcore-java all 4.4.11-1 [625 kB] Get: 202 http://deb.debian.org/debian buster/main amd64 libcommons-codec-java all 1.11-1 [271 kB] Get: 203 http://deb.debian.org/debian buster/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 204 http://deb.debian.org/debian buster/main amd64 libhttpclient-java all 4.5.7-1+deb10u1 [721 kB] Get: 205 http://deb.debian.org/debian buster/main amd64 libjsoup-java all 1.10.2-2 [350 kB] Get: 206 http://deb.debian.org/debian buster/main amd64 libwagon-http-java all 3.3.1-2 [50.5 kB] Get: 207 http://deb.debian.org/debian buster/main amd64 libistack-commons-java all 3.0.6-3 [144 kB] Get: 208 http://deb.debian.org/debian buster/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-8 [163 kB] Get: 209 http://deb.debian.org/debian buster/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 210 http://deb.debian.org/debian buster/main amd64 libcommons-pool-java all 1.6-3 [104 kB] Get: 211 http://deb.debian.org/debian buster/main amd64 libcommons-dbcp-java all 1.4-6 [157 kB] Get: 212 http://deb.debian.org/debian buster/main amd64 libcommons-math-java all 2.2-7 [928 kB] Get: 213 http://deb.debian.org/debian buster/main amd64 libdtd-parser-java all 1.2~svn20110404-1 [62.5 kB] Get: 214 http://deb.debian.org/debian buster/main amd64 libel-api-java all 3.0.0-2+deb10u1 [64.9 kB] Get: 215 http://deb.debian.org/debian buster/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 216 http://deb.debian.org/debian buster/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 217 http://deb.debian.org/debian buster/main amd64 libstreambuffer-java all 1.5.4-1 [71.8 kB] Get: 218 http://deb.debian.org/debian buster/main amd64 librelaxng-datatype-java all 1.0+ds1-3 [11.7 kB] Get: 219 http://deb.debian.org/debian buster/main amd64 libxsom-java all 2.3.0.1-8 [396 kB] Get: 220 http://deb.debian.org/debian buster/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 221 http://deb.debian.org/debian buster/main amd64 libgoogle-gson-java all 2.8.5-3 [225 kB] Get: 222 http://deb.debian.org/debian buster/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 223 http://deb.debian.org/debian buster/main amd64 libjsp-api-java all 2.3.4-2+deb10u1 [53.7 kB] Get: 224 http://deb.debian.org/debian buster/main amd64 libwebsocket-api-java all 1.1-1+deb10u1 [40.0 kB] Get: 225 http://deb.debian.org/debian buster/main amd64 libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 226 http://deb.debian.org/debian buster/main amd64 libhsqldb-java all 2.4.1-2 [1633 kB] Get: 227 http://deb.debian.org/debian buster/main amd64 libitext5-java all 5.5.13-1 [2620 kB] Get: 228 http://deb.debian.org/debian buster/main amd64 librngom-java all 2.3.0.1-8 [288 kB] Get: 229 http://deb.debian.org/debian buster/main amd64 libtxw2-java all 2.3.0.1-8 [134 kB] Get: 230 http://deb.debian.org/debian buster/main amd64 libxml-commons-resolver1.1-java all 1.2-9 [91.6 kB] Get: 231 http://deb.debian.org/debian buster/main amd64 libjaxb-java all 2.3.0.1-8 [1966 kB] Get: 232 http://deb.debian.org/debian buster/main amd64 libjaxp1.3-java all 1.3.05-5 [226 kB] Get: 233 http://deb.debian.org/debian buster/main amd64 libjgraph-java all 5.12.4.2+dfsg-5 [205 kB] Get: 234 http://deb.debian.org/debian buster/main amd64 libjgrapht0.8-java all 0.8.3-5 [214 kB] Get: 235 http://deb.debian.org/debian buster/main amd64 libnaga-java all 3.0+svn80-2 [884 kB] Get: 236 http://deb.debian.org/debian buster/main amd64 libjmol-java all 14.6.4+2016.11.05+dfsg1-4 [6393 kB] Get: 237 http://deb.debian.org/debian buster/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 238 http://deb.debian.org/debian buster/main amd64 liblightcouch-java all 0.0.6-1 [63.7 kB] Get: 239 http://deb.debian.org/debian buster/main amd64 liblog4j2-java all 2.11.1-2 [1721 kB] Get: 240 http://deb.debian.org/debian buster/main amd64 libnetx-java all 0.5-4 [138 kB] Get: 241 http://deb.debian.org/debian buster/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 242 http://deb.debian.org/debian buster/main amd64 libxmlunit-java all 1.6-1 [95.5 kB] Get: 243 http://deb.debian.org/debian buster/main amd64 rdfind amd64 1.4.1-1 [40.4 kB] Fetched 362 MB in 7s (48.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../1-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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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:amd64 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libxcb1:amd64 (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:amd64 (0.7-4+deb10u1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up libnet-http-perl (6.18-1) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... 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 (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libmaven-resolver-java (1.3.1-1) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... 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:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (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+deb10u1) ... Setting up libsisu-guice-java (4.2.0-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... 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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:amd64 (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:amd64 (2.2.10-6+deb10u4) ... Setting up libhttpclient-java (4.5.7-1+deb10u1) ... 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:amd64 (2.13.1-2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libplexus-io-java (3.1.1-1) ... Setting up libxi6:amd64 (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:amd64 (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:amd64 (11.0.9.1+1-1~deb10u2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jdk-headless:amd64 (11.0.9.1+1-1~deb10u2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up 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:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Taiwan_GRCA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.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 (20200601~deb10u2) ... 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" HOME="/nonexistent/first-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 amd64 fakeroot debian/rules clean dh clean --with javahelper jh_clean debian/rules override_dh_clean make[1]: Entering 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]: Leaving 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]: Entering 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]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' jh_linkjars debian/rules override_dh_auto_build make[1]: Entering 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: 3 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: 15 seconds 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: 6 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: 3 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: 4 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: 3 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: 4 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: 3 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: 13 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: 6 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: 3 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: 3 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: 3 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: 2 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: 2 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: 4 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... 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[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 11.0.9.1 [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: 27 seconds # rm -rf biojavadoc make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' debian/rules override_dh_auto_test make[1]: Entering 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 11.0.9.1 [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: 0.126 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.126 sec [junit] [junit] Testcase: testGetIndexOf took 0.043 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetNumGaps took 0.001 sec [junit] Testcase: testGetStart took 0 sec [junit] Testcase: testGetSequenceIndexAt took 0.001 sec [junit] Testcase: testGetAccession took 0.001 sec [junit] Testcase: testToString took 0.004 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0 sec [junit] Testcase: testCountCompounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAt took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.002 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.004 sec [junit] Testcase: testGetOriginalSequence took 0 sec [junit] Testcase: testGetCompoundAt took 0 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetEnd took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceLocal took 0 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0 sec [junit] Testcase: testGetOverlapCount took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetLocationInAlignment took 0.002 sec [junit] Testcase: testIterator took 0 sec [junit] Testcase: testGetSequenceAsString took 0.001 sec [junit] Testcase: testGetLastIndexOf took 0 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.002 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: 0.225 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.225 sec [junit] [junit] Testcase: testGetIndexOf took 0.083 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequenceInt took 0.002 sec [junit] Testcase: testToStringInt took 0.012 sec [junit] Testcase: testToString took 0.001 sec [junit] Testcase: testToStringFormatted took 0.031 sec [junit] Testcase: testSimpleProfile took 0 sec [junit] Testcase: testGetSize took 0 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec [junit] Testcase: testGetAlignedSequences took 0.001 sec [junit] Testcase: testGetOriginalSequences took 0 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0 sec [junit] Testcase: testGetAlignedSequencesSArray took 0 sec [junit] Testcase: testGetIndicesAt took 0.002 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.002 sec [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec [junit] Testcase: testGetLength took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundSet took 0.001 sec [junit] Testcase: testGetCompoundsAt took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0 sec [junit] Testcase: testIterator took 0.001 sec [junit] Testcase: testGetLastIndexOf took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0.001 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: 0.162 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.162 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.082 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetCompoundInQueryAt took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumIdenticals took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInTargetAt took 0 sec [junit] Testcase: testGetIndexInQueryAt took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumSimilars took 0.002 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 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: 0.146 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetAlignment took 0.08 sec [junit] Testcase: testHashCode took 0.001 sec [junit] Testcase: testEquals took 0 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: 0.413 sec [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.413 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] Apr 06, 2021 7:28:30 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Apr 06, 2021 7:28:30 PM 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 0.219 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 0.146 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0.006 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: 9 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 11.0.9.1 [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: 0.164 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 sec [junit] [junit] Testcase: testGetQuery took 0.086 sec [junit] Testcase: testGetScore took 0.038 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 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: 0.185 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.185 sec [junit] [junit] Testcase: testGetQuery took 0.089 sec [junit] Testcase: testGetScore took 0.054 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.002 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 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: 0.466 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.466 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 0.212 sec [junit] Testcase: testToString took 0.005 sec [junit] Testcase: testGetScoreMatrix took 0.007 sec [junit] Testcase: testGetRoot took 0.168 sec [junit] Testcase: testGetSequences took 0.004 sec [junit] Testcase: testGetDistanceMatrix took 0.005 sec [junit] Testcase: testGetAllPairsScores took 0.003 sec [junit] Testcase: testIterator took 0.002 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: 0.212 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.212 sec [junit] [junit] Testcase: shouldAllowZeroLengthMatches took 0.174 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: 0.64 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.64 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.093 sec [junit] Testcase: testGetGapPenalty took 0.001 sec [junit] Testcase: testGetComputationTime took 0.063 sec [junit] Testcase: should_align_middle_anchor took 0.049 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec [junit] Testcase: should_align_all_anchored took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.002 sec [junit] Testcase: should_align_multiple_anchors took 0.002 sec [junit] Testcase: testAnchoredDNAAlignment took 0.006 sec [junit] Testcase: testGetProfile took 0.003 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: should_align_ending_anchor took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec [junit] Testcase: testComplex took 0.012 sec [junit] Testcase: testGetScoreMatrixAsString took 0.027 sec [junit] Testcase: should_align_starting_anchor took 0.001 sec [junit] Testcase: anchors_should_not_change_score took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0 sec [junit] Testcase: testIntOverflowBug took 0.278 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: 0.049 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec [junit] [junit] Testcase: testOpenPenalty took 0.003 sec [junit] Testcase: testType took 0 sec [junit] Testcase: testExtensionPenalty took 0 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec [junit] Testcase: testSimpleGapPenalty took 0 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: 0.19 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 sec [junit] [junit] Testcase: testGetQuery took 0.139 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testSimpleProfilePair took 0.007 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: 0.284 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.141 sec [junit] Testcase: testGetGapPenalty took 0.006 sec [junit] Testcase: testGetComputationTime took 0.005 sec [junit] Testcase: testGetQuery took 0.005 sec [junit] Testcase: testGetScore took 0.004 sec [junit] Testcase: testGetScoreMatrix took 0.005 sec [junit] Testcase: testGetPair took 0.01 sec [junit] Testcase: testGetProfile took 0.005 sec [junit] Testcase: testGetMinScore took 0.003 sec [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec [junit] Testcase: testGetScoreMatrixAsString took 0.043 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.003 sec [junit] Testcase: testSimpleProfileProfileAligner took 0.002 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.002 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: 0.217 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.217 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.012 sec [junit] Testcase: testSetDescription took 0.036 sec [junit] Testcase: testToString took 0.053 sec [junit] Testcase: testCaseEquivalence took 0.002 sec [junit] Testcase: test took 0.019 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.019 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.004 sec [junit] Testcase: testSetName took 0.008 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.004 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: 0.267 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.102 sec [junit] Testcase: testGetGapPenalty took 0.001 sec [junit] Testcase: testGetComputationTime took 0.036 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.003 sec [junit] Testcase: testGetScoreMatrix took 0.002 sec [junit] Testcase: testGetPair took 0.008 sec [junit] Testcase: testSmithWaterman took 0.001 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.052 sec [junit] Testcase: testSetStoringScoreMatrix took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 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: 0.049 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec [junit] [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.004 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.002 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0.001 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0 sec [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0.001 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 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: 0.189 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.189 sec [junit] [junit] Testcase: testGetComputationTime took 0.105 sec [junit] Testcase: testGuanUberbacher took 0.002 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testGetPair took 0.005 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: should_align_shorter_target took 0.031 sec [junit] Testcase: should_align_multiple_cuts took 0.001 sec [junit] Testcase: testGetMaxScore took 0 sec [junit] Testcase: should_align_shorter_query took 0 sec BUILD SUCCESSFUL Total time: 17 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 11.0.9.1 [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: 0.774 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.774 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 0.652 sec [junit] Testcase: testExample1 took 0.032 sec [junit] Testcase: testExample2 took 0.009 sec [junit] Testcase: testExample3 took 0.007 sec [junit] Testcase: testExample1WithCSV took 0.026 sec [junit] Testcase: testWithCases took 0.011 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: 0.753 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.753 sec [junit] [junit] Testcase: shortExample1 took 0.03 sec [junit] Testcase: shortExample2 took 0.588 sec [junit] Testcase: shortExample3 took 0.074 sec [junit] Testcase: shortExample4 took 0.002 sec [junit] Testcase: shortExample5 took 0.006 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: 0.871 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.871 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 0.75 sec [junit] Testcase: testExample1 took 0.028 sec [junit] Testcase: testExample2 took 0.016 sec [junit] Testcase: testExample3 took 0.013 sec [junit] Testcase: testExample1WithCSV took 0.018 sec [junit] Testcase: testWithCases took 0.011 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: 1.069 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.069 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 0.034 sec [junit] Testcase: testMolecularWeightXMLSingleFile took 0.65 sec [junit] Testcase: testEnrichment took 0.02 sec [junit] Testcase: testApliphaticIndex took 0.002 sec [junit] Testcase: testMolecularWeightXMLNull took 0.01 sec [junit] Testcase: testApliphaticIndexNull took 0 sec [junit] Testcase: testIsoelectricPointExpasy took 0.003 sec [junit] Testcase: testAbsorbanceNull took 0 sec [junit] Testcase: testIsoelectricPointNull took 0.001 sec [junit] Testcase: testAverageHydropathy took 0.001 sec [junit] Testcase: testExtinctionCoefficient took 0.002 sec [junit] Testcase: testAAComposition took 0.002 sec [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.055 sec [junit] Testcase: testMolecularWeight took 0.002 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.003 sec [junit] Testcase: testNetChargeNull took 0 sec [junit] Testcase: testExtinctionCoefficientNull took 0 sec [junit] Testcase: testNetCharge took 0.145 sec [junit] Testcase: testEnrichmentNull took 0 sec [junit] Testcase: testInstabilityIndexNull took 0 sec [junit] Testcase: testAverageHydropathyNull took 0 sec [junit] Testcase: testMolecularWeightXML took 0.074 sec [junit] Testcase: testInstabilityIndex took 0.001 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: 0.032 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] [junit] Testcase: testFake took 0.002 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: 0.059 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec [junit] [junit] Testcase: testFakeTest took 0.001 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: 0.917 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.917 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 0.45 sec [junit] Testcase: readWithIDXml took 0.201 sec [junit] Testcase: readMinXml took 0.079 sec [junit] Testcase: readAdvancedXml took 0.041 sec [junit] Testcase: generateXml took 0.039 sec [junit] Testcase: readXml took 0.075 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: 0.821 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.821 sec [junit] [junit] Testcase: generateSchema took 0.47 sec [junit] Testcase: generateXml took 0.086 sec [junit] Testcase: readXml took 0.213 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: 0.062 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 sec [junit] [junit] Testcase: testFake took 0.001 sec BUILD SUCCESSFUL Total time: 15 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 11.0.9.1 BUILD SUCCESSFUL Total time: 3 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 11.0.9.1 [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: 0.142 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 sec [junit] [junit] Testcase: testConvert took 0.127 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: 0.026 sec [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] [junit] Testcase: testBuildAppendSequence took 0.004 sec [junit] Testcase: testBuildNullDescription took 0.001 sec [junit] Testcase: testBuildAppendQuality took 0 sec [junit] Testcase: testBuild took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0 sec [junit] Testcase: testBuildNullSequence took 0 sec [junit] Testcase: testBuildMissingDescription took 0 sec [junit] Testcase: testBuildNullVariant took 0 sec [junit] Testcase: testBuildDefault took 0 sec [junit] Testcase: testBuildMissingSequence took 0.001 sec [junit] Testcase: testBuildNullQuality took 0 sec [junit] Testcase: testBuildMultiple took 0.001 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: 0.025 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] [junit] Testcase: testImmutable took 0.001 sec [junit] Testcase: testBuilder took 0.002 sec [junit] Testcase: testVariant took 0 sec [junit] Testcase: testQuality took 0.003 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0 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: 0.102 sec [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.102 sec [junit] [junit] Testcase: testErrorProbabilitiesNullFastq took 0.002 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.001 sec [junit] Testcase: testConvertNullVariant took 0 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.062 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec [junit] Testcase: testCreateQualityScores took 0.001 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec [junit] Testcase: testConvertQualitiesNullFastq took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.001 sec [junit] Testcase: testConvertQualitiesNullVariant took 0.001 sec [junit] Testcase: testConvertSameVariant took 0 sec [junit] Testcase: testQualityScores took 0.005 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec [junit] Testcase: testCreateDNASequence took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec [junit] Testcase: testQualityScoresIntArray took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testToList took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec [junit] Testcase: testErrorProbabilities took 0 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: 0.024 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec [junit] [junit] Testcase: testParseFastqVariant took 0.003 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec [junit] Testcase: testIsSanger took 0.003 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec [junit] Testcase: testIsSolexa took 0 sec [junit] Testcase: testIsIllumina took 0.001 sec [junit] Testcase: testDescription took 0 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: 0.193 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 sec [junit] [junit] Testcase: testFullRangeAsIllumina took 0.058 sec [junit] Testcase: testWrappingAsIllumina took 0.005 sec [junit] Testcase: testValidateDescription took 0.011 sec [junit] Testcase: testValidateRepeatDescription took 0.004 sec [junit] Testcase: testMiscDnaAsIllumina took 0.003 sec [junit] Testcase: testMiscRnaAsIllumina took 0.003 sec [junit] Testcase: testLongReadsAsIllumina took 0.005 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.024 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.035 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.002 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0.001 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0 sec [junit] Testcase: testReadRoundTripMultipleFile took 0 sec [junit] Testcase: testWrappedQuality took 0.001 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: 0.06 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.009 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec [junit] Testcase: testWriteFileIterable took 0.022 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.002 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: 0.165 sec [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 sec [junit] [junit] Testcase: testMiscRnaAsSanger took 0.044 sec [junit] Testcase: testFullRangeAsSanger took 0.005 sec [junit] Testcase: testWrappingOriginal took 0.004 sec [junit] Testcase: testLongReadsOriginal took 0.009 sec [junit] Testcase: testMiscDnaOriginal took 0.003 sec [junit] Testcase: testMiscRnaOriginal took 0.002 sec [junit] Testcase: testValidateDescription took 0.008 sec [junit] Testcase: testValidateRepeatDescription took 0.003 sec [junit] Testcase: testFullRangeOriginal took 0.002 sec [junit] Testcase: testWrappingAsSanger took 0.002 sec [junit] Testcase: testLongReadsAsSanger took 0.004 sec [junit] Testcase: testMiscDnaAsSanger took 0.002 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.024 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.023 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0.001 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testReadEmptyURL took 0 sec [junit] Testcase: testReadRoundTripMultipleFile took 0 sec [junit] Testcase: testWrappedQuality took 0.001 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: 0.059 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec [junit] [junit] Testcase: testConvertNotSangerVariant took 0.009 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testWriteOutputStreamVararg took 0.005 sec [junit] Testcase: testWriteFileIterable took 0.021 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.002 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: 0.15 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 sec [junit] [junit] Testcase: testMiscRnaAsSolexa took 0.04 sec [junit] Testcase: testFullRangeAsSolexa took 0.004 sec [junit] Testcase: testValidateDescription took 0.01 sec [junit] Testcase: testValidateRepeatDescription took 0.003 sec [junit] Testcase: testWrappingAsSolexa took 0.003 sec [junit] Testcase: testLongReadsAsSolexa took 0.005 sec [junit] Testcase: testMiscDnaAsSolexa took 0.003 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.023 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.028 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testReadEmptyURL took 0 sec [junit] Testcase: testReadRoundTripMultipleFile took 0 sec [junit] Testcase: testWrappedQuality took 0.001 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: 0.05 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec [junit] [junit] Testcase: testConvertNotSolexaVariant took 0.007 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec [junit] Testcase: testWriteFileIterable took 0.017 sec [junit] Testcase: testWriteOutputStreamIterable took 0 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.001 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: 0.023 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec [junit] [junit] Testcase: testStreamNullVariant took 0.002 sec [junit] Testcase: testStreamNullListener took 0.003 sec [junit] Testcase: testStreamNullReadable took 0.001 sec BUILD SUCCESSFUL Total time: 11 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 11.0.9.1 [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: 0.017 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] [junit] Testcase: testMe took 0.001 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: 0.018 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] [junit] Testcase: testSomeMethod took 0.001 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: 0.023 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec [junit] [junit] Testcase: testGetColor took 0.004 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec [junit] Testcase: testGetSelection took 0.002 sec [junit] Testcase: testRepaint took 0 sec [junit] Testcase: testSetSelection took 0 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec [junit] Testcase: testSetStyle took 0 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: 0.017 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL Total time: 5 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 11.0.9.1 BUILD SUCCESSFUL Total time: 2 seconds make[1]: Leaving 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]: Entering 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 10341 files. Now scanning "debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java", found 1873 files. Now have 12214 files in total. Removed 0 files due to nonunique device and inode. Total size is 322383940 bytes or 307 MiB Removed 7253 files due to unique sizes from list.4961 files left. Now eliminating candidates based on first bytes:removed 767 files from list.4194 files left. Now eliminating candidates based on last bytes:removed 19 files from list.4175 files left. Now eliminating candidates based on sha1 checksum:removed 4137 files from list.38 files left. It seems like you have 38 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-3.5.1.js Making 19 links. make[1]: Leaving 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: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-2_all.deb'. dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-2_all.deb'. dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava4-live_4.2.12+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/48295 and its subdirectories I: Current time: Tue Apr 6 19:30:04 -12 2021 I: pbuilder-time-stamp: 1617780604