Mon Jul 20 05:09:05 UTC 2020 I: starting to build biojava4-live/buster/i386 on jenkins on '2020-07-20 05:08' Mon Jul 20 05:09:05 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/4211/console.log Mon Jul 20 05:09:05 UTC 2020 I: Downloading source for buster/biojava4-live=4.2.12+dfsg-2 --2020-07-20 05:09:05-- http://deb.debian.org/debian/pool/main/b/biojava4-live/biojava4-live_4.2.12+dfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2699 (2.6K) Saving to: ‘biojava4-live_4.2.12+dfsg-2.dsc’ 0K .. 100% 194M=0s 2020-07-20 05:09:05 (194 MB/s) - ‘biojava4-live_4.2.12+dfsg-2.dsc’ saved [2699/2699] Mon Jul 20 05:09:05 UTC 2020 I: biojava4-live_4.2.12+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: biojava4-live Binary: libbiojava4.0-java, libbiojava4-java, libbiojava4-java-doc Architecture: all Version: 4.2.12+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Homepage: http://www.biojava.org Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/biojava4-live Vcs-Git: https://salsa.debian.org/med-team/biojava4-live.git Build-Depends: debhelper (>= 11~), ant Build-Depends-Indep: 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 Package-List: libbiojava4-java deb java optional arch=all libbiojava4-java-doc deb doc optional arch=all libbiojava4.0-java deb java optional arch=all Checksums-Sha1: 35482e33f668eb4de9b371c93ed510f612d09281 12178028 biojava4-live_4.2.12+dfsg.orig.tar.xz 96cb85443951da5a753e8da201395e7ffaed6a5b 15048 biojava4-live_4.2.12+dfsg-2.debian.tar.xz Checksums-Sha256: 63ea99c016b4bbb87a62c9cb05d0dbc352845851c200b676821037d76c6021c7 12178028 biojava4-live_4.2.12+dfsg.orig.tar.xz 015bb633800dfcbf5cce8f764debc612243a353441e65d598ccc1edfb4467c0c 15048 biojava4-live_4.2.12+dfsg-2.debian.tar.xz Files: c66ea841163dc423be3713cf937cef2a 12178028 biojava4-live_4.2.12+dfsg.orig.tar.xz 82183773c128d9e923d975604111cd5d 15048 biojava4-live_4.2.12+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAlxCLY0ACgkQPCZ2P2xn 5uL9ThAAtUzeiJo3kZUw2GyOBPhrj+2B1WxIVia1tqBG40zFhm+Y3XotIAHw0ZwA 8ibG83jDRkKAD7x1Iowxz9wJIDHaBoslprCTXP05kHNvPTblaeksnvVF8e4sRPPU wN7DUrjhU7w+z+jHH/mBLemxy+it4EdgB4NkOOjBiv4UEldleK6p9yz/GwOsZkOG PMk5YPiPE9Zt5cwkO+7MlJrSkvJIjitLaB0GW6eJxR2vcQFZoyYmaACbIPYYsDxL rGQGoyxkELR1RfEjsoiFYqs9piZzYpr+6g9oxilHRrMGglAOzxkoWOyzky7xHfl7 dyj/t20ASXA1d7toXhYzSlWIhyRbIW9o52YCft2UA5NueZpSAyfQG+w6VMRSSd4S RKNGB1ztdNSz0bWBu3mRbg8gJcw8Xa0nE31kZ0qhYXgUbSf0EuzC03p4Ql6X3gYK cJp2BRtQ1phexUcg5smy6QnVDDk9louQDyPzE9Lul0pVfHz2BExJR5z0wwgFAo2E 4iIzLx/ALCAG7cLE4cLaDzewGYGkg0ErIRH1NKMBhlucGN3RIw1xO5QWvvuNpDVn j0Hv4xfZ37aaE6xpfEq46ij5sXaG5Z5rP0vjL1epEnBhKmoCeDfLSDcrnszJ7snw sOnkZ3dR4pQrDJXFkpEoWFkwbFyg32VjemLPnfeZ/u8ItnWE6i8= =4gVx -----END PGP SIGNATURE----- Mon Jul 20 05:09:05 UTC 2020 I: Checking whether the package is not for us Mon Jul 20 05:09:05 UTC 2020 I: Starting 1st build on remote node profitbricks-build16-i386.debian.net. Mon Jul 20 05:09:05 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build16-i386.debian.net. Mon Jul 20 05:11:45 UTC 2020 I: Deleting $TMPDIR on profitbricks-build16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 21 23:32:04 -12 2021 I: pbuilder-time-stamp: 1629631924 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: using eatmydata during job 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/61522/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='0ac6d1b28f734842a887d4390a220fa4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='61522' 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.ueqfUSB33L/pbuilderrc_UBAR --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux profitbricks-build16-i386 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 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 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 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 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 206392 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 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 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 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 21 02:47 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 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/61522/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: i386 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 ... 19234 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 412 MB of archives. After unpacking 941 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libpython3.7-minimal i386 3.7.3-2+deb10u1 [590 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-2+deb10u1 [104 kB] Get: 10 http://deb.debian.org/debian buster/main i386 python3.7-minimal i386 3.7.3-2+deb10u1 [1745 kB] Get: 11 http://deb.debian.org/debian buster/main i386 python3-minimal i386 3.7.3-1 [36.6 kB] Get: 12 http://deb.debian.org/debian buster/main i386 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libmpdec2 i386 2.4.2-2 [83.2 kB] Get: 14 http://deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libpython3.7-stdlib i386 3.7.3-2+deb10u1 [1750 kB] Get: 17 http://deb.debian.org/debian buster/main i386 python3.7 i386 3.7.3-2+deb10u1 [330 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libpython3-stdlib i386 3.7.3-1 [20.0 kB] Get: 19 http://deb.debian.org/debian buster/main i386 python3 i386 3.7.3-1 [61.5 kB] Get: 20 http://deb.debian.org/debian buster/main i386 netbase all 5.6 [19.4 kB] Get: 21 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 24 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 25 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 26 http://deb.debian.org/debian buster/main i386 ucf all 3.0038+nmu1 [69.0 kB] Get: 27 http://deb.debian.org/debian buster/main i386 openssl i386 1.1.1d-0+deb10u3 [853 kB] Get: 28 http://deb.debian.org/debian buster/main i386 ca-certificates all 20190110 [157 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libnspr4 i386 2:4.20-1 [122 kB] Get: 30 http://deb.debian.org/debian buster/main i386 libnss3 i386 2:3.42.1-1+deb10u2 [1237 kB] Get: 31 http://deb.debian.org/debian buster/main i386 ca-certificates-java all 20190405 [15.7 kB] Get: 32 http://deb.debian.org/debian buster/main i386 java-common all 0.71 [14.4 kB] Get: 33 http://deb.debian.org/debian buster/main i386 libavahi-common-data i386 0.7-4+b1 [122 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libavahi-common3 i386 0.7-4+b1 [56.2 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libdbus-1-3 i386 1.12.16-1 [226 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libavahi-client3 i386 0.7-4+b1 [60.1 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libkeyutils1 i386 1.6-6 [15.4 kB] Get: 38 http://deb.debian.org/debian buster/main i386 libkrb5support0 i386 1.17-3 [68.6 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libk5crypto3 i386 1.17-3 [126 kB] Get: 40 http://deb.debian.org/debian buster/main i386 libkrb5-3 i386 1.17-3 [396 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libgssapi-krb5-2 i386 1.17-3 [168 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libcups2 i386 2.2.10-6+deb10u3 [338 kB] Get: 43 http://deb.debian.org/debian buster/main i386 liblcms2-2 i386 2.9-3 [156 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libjpeg62-turbo i386 1:1.5.2-2+b1 [142 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libpng16-16 i386 1.6.36-6 [301 kB] Get: 46 http://deb.debian.org/debian buster/main i386 libfreetype6 i386 2.9.1-3+deb10u1 [395 kB] Get: 47 http://deb.debian.org/debian buster/main i386 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 48 http://deb.debian.org/debian buster/main i386 fontconfig-config all 2.13.1-2 [280 kB] Get: 49 http://deb.debian.org/debian buster/main i386 libfontconfig1 i386 2.13.1-2 [357 kB] Get: 50 http://deb.debian.org/debian buster/main i386 libasound2-data all 1.1.8-1 [59.6 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libasound2 i386 1.1.8-1 [382 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libpcsclite1 i386 1.8.24-1 [60.0 kB] Get: 53 http://deb.debian.org/debian buster/main i386 libxau6 i386 1:1.0.8-1+b2 [20.3 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 55 http://deb.debian.org/debian buster/main i386 libxcb1 i386 1.13.1-2 [141 kB] Get: 56 http://deb.debian.org/debian buster/main i386 libx11-data all 2:1.6.7-1 [298 kB] Get: 57 http://deb.debian.org/debian buster/main i386 libx11-6 i386 2:1.6.7-1 [778 kB] Get: 58 http://deb.debian.org/debian buster/main i386 libxext6 i386 2:1.3.3-1+b2 [55.2 kB] Get: 59 http://deb.debian.org/debian buster/main i386 libxi6 i386 2:1.7.9-1 [85.2 kB] Get: 60 http://deb.debian.org/debian buster/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 61 http://deb.debian.org/debian buster/main i386 lsb-base all 10.2019051400 [28.4 kB] Get: 62 http://deb.debian.org/debian buster/main i386 x11-common all 1:7.7+19 [251 kB] Get: 63 http://deb.debian.org/debian buster/main i386 libxtst6 i386 2:1.2.3-1 [28.3 kB] Get: 64 http://deb.debian.org/debian buster/main i386 openjdk-11-jre-headless i386 11.0.6+10-1~deb10u1 [36.9 MB] Get: 65 http://deb.debian.org/debian buster/main i386 default-jre-headless i386 2:1.11-71 [10.9 kB] Get: 66 http://deb.debian.org/debian buster/main i386 ant all 1.10.5-2 [2082 kB] Get: 67 http://deb.debian.org/debian buster/main i386 ant-contrib all 1.0~b3+svn177-10 [262 kB] Get: 68 http://deb.debian.org/debian buster/main i386 ant-optional all 1.10.5-2 [379 kB] Get: 69 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 70 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 71 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 72 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 73 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 74 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 75 http://deb.debian.org/debian buster/main i386 dctrl-tools i386 2.24-3 [105 kB] Get: 76 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 77 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 78 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 79 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 80 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 81 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 82 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 83 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 84 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 85 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 86 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 87 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 88 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 89 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 90 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 91 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 92 http://deb.debian.org/debian buster/main i386 openjdk-11-doc all 11.0.6+10-1~deb10u1 [13.5 MB] Get: 93 http://deb.debian.org/debian buster/main i386 default-jdk-doc i386 2:1.11-71 [10.9 kB] Get: 94 http://deb.debian.org/debian buster/main i386 openjdk-11-jdk-headless i386 11.0.6+10-1~deb10u1 [280 MB] Get: 95 http://deb.debian.org/debian buster/main i386 default-jdk-headless i386 2:1.11-71 [1104 B] Get: 96 http://deb.debian.org/debian buster/main i386 libassuan0 i386 2.5.2-1 [51.5 kB] Get: 97 http://deb.debian.org/debian buster/main i386 gpgconf i386 2.2.12-1+deb10u1 [517 kB] Get: 98 http://deb.debian.org/debian buster/main i386 libksba8 i386 1.3.5-2 [107 kB] Get: 99 http://deb.debian.org/debian buster/main i386 libsasl2-modules-db i386 2.1.27+dfsg-1+deb10u1 [70.1 kB] Get: 100 http://deb.debian.org/debian buster/main i386 libsasl2-2 i386 2.1.27+dfsg-1+deb10u1 [110 kB] Get: 101 http://deb.debian.org/debian buster/main i386 libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 102 http://deb.debian.org/debian buster/main i386 libldap-2.4-2 i386 2.4.47+dfsg-3+deb10u2 [236 kB] Get: 103 http://deb.debian.org/debian buster/main i386 libnpth0 i386 1.6-1 [18.7 kB] Get: 104 http://deb.debian.org/debian buster/main i386 dirmngr i386 2.2.12-1+deb10u1 [738 kB] Get: 105 http://deb.debian.org/debian buster/main i386 gnupg-l10n all 2.2.12-1+deb10u1 [1010 kB] Get: 106 http://deb.debian.org/debian buster/main i386 gnupg-utils i386 2.2.12-1+deb10u1 [908 kB] Get: 107 http://deb.debian.org/debian buster/main i386 gpg i386 2.2.12-1+deb10u1 [905 kB] Get: 108 http://deb.debian.org/debian buster/main i386 pinentry-curses i386 1.1.0-2 [66.3 kB] Get: 109 http://deb.debian.org/debian buster/main i386 gpg-agent i386 2.2.12-1+deb10u1 [636 kB] Get: 110 http://deb.debian.org/debian buster/main i386 gpg-wks-client i386 2.2.12-1+deb10u1 [496 kB] Get: 111 http://deb.debian.org/debian buster/main i386 gpg-wks-server i386 2.2.12-1+deb10u1 [487 kB] Get: 112 http://deb.debian.org/debian buster/main i386 gpgsm i386 2.2.12-1+deb10u1 [624 kB] Get: 113 http://deb.debian.org/debian buster/main i386 gnupg all 2.2.12-1+deb10u1 [715 kB] Get: 114 http://deb.debian.org/debian buster/main i386 libfile-which-perl all 1.23-1 [16.6 kB] Get: 115 http://deb.debian.org/debian buster/main i386 libfile-homedir-perl all 1.004-1 [42.7 kB] Get: 116 http://deb.debian.org/debian buster/main i386 libio-pty-perl i386 1:1.08-1.1+b5 [34.4 kB] Get: 117 http://deb.debian.org/debian buster/main i386 libipc-run-perl all 20180523.0-1 [101 kB] Get: 118 http://deb.debian.org/debian buster/main i386 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get: 119 http://deb.debian.org/debian buster/main i386 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get: 120 http://deb.debian.org/debian buster/main i386 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get: 121 http://deb.debian.org/debian buster/main i386 libb-hooks-op-check-perl i386 0.22-1+b1 [11.5 kB] Get: 122 http://deb.debian.org/debian buster/main i386 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get: 123 http://deb.debian.org/debian buster/main i386 libdevel-callchecker-perl i386 0.008-1 [15.7 kB] Get: 124 http://deb.debian.org/debian buster/main i386 libparams-classify-perl i386 0.015-1+b1 [26.1 kB] Get: 125 http://deb.debian.org/debian buster/main i386 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 126 http://deb.debian.org/debian buster/main i386 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 127 http://deb.debian.org/debian buster/main i386 librole-tiny-perl all 2.000006-1 [19.4 kB] Get: 128 http://deb.debian.org/debian buster/main i386 libstrictures-perl all 2.000005-1 [18.3 kB] Get: 129 http://deb.debian.org/debian buster/main i386 libsub-quote-perl all 2.005001-1 [17.9 kB] Get: 130 http://deb.debian.org/debian buster/main i386 libmoo-perl all 2.003004-2 [57.4 kB] Get: 131 http://deb.debian.org/debian buster/main i386 libencode-locale-perl all 1.05-1 [13.7 kB] Get: 132 http://deb.debian.org/debian buster/main i386 libtimedate-perl all 2.3000-2+deb10u1 [38.1 kB] Get: 133 http://deb.debian.org/debian buster/main i386 libhttp-date-perl all 6.02-1 [10.7 kB] Get: 134 http://deb.debian.org/debian buster/main i386 libfile-listing-perl all 6.04-1 [10.3 kB] Get: 135 http://deb.debian.org/debian buster/main i386 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 136 http://deb.debian.org/debian buster/main i386 liburi-perl all 1.76-1 [89.9 kB] Get: 137 http://deb.debian.org/debian buster/main i386 libhtml-parser-perl i386 3.72-3+b3 [106 kB] Get: 138 http://deb.debian.org/debian buster/main i386 libhtml-tree-perl all 5.07-2 [213 kB] Get: 139 http://deb.debian.org/debian buster/main i386 libio-html-perl all 1.001-1 [17.6 kB] Get: 140 http://deb.debian.org/debian buster/main i386 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get: 141 http://deb.debian.org/debian buster/main i386 libhttp-message-perl all 6.18-1 [77.8 kB] Get: 142 http://deb.debian.org/debian buster/main i386 libhttp-cookies-perl all 6.04-1 [17.8 kB] Get: 143 http://deb.debian.org/debian buster/main i386 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 144 http://deb.debian.org/debian buster/main i386 perl-openssl-defaults i386 3 [6782 B] Get: 145 http://deb.debian.org/debian buster/main i386 libnet-ssleay-perl i386 1.85-2+b1 [314 kB] Get: 146 http://deb.debian.org/debian buster/main i386 libio-socket-ssl-perl all 2.060-3 [207 kB] Get: 147 http://deb.debian.org/debian buster/main i386 libnet-http-perl all 6.18-1 [24.5 kB] Get: 148 http://deb.debian.org/debian buster/main i386 liblwp-protocol-https-perl all 6.07-2 [9242 B] Get: 149 http://deb.debian.org/debian buster/main i386 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 150 http://deb.debian.org/debian buster/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 151 http://deb.debian.org/debian buster/main i386 libwww-perl all 6.36-2 [188 kB] Get: 152 http://deb.debian.org/debian buster/main i386 patchutils i386 0.3.4-2 [92.4 kB] Get: 153 http://deb.debian.org/debian buster/main i386 wdiff i386 1.2.2-2+b1 [123 kB] Get: 154 http://deb.debian.org/debian buster/main i386 devscripts i386 2.19.5+deb10u1 [1046 kB] Get: 155 http://deb.debian.org/debian buster/main i386 javahelper all 0.72.9 [96.4 kB] Get: 156 http://deb.debian.org/debian buster/main i386 junit all 3.8.2-9 [110 kB] Get: 157 http://deb.debian.org/debian buster/main i386 libhamcrest-java all 1.3-9 [388 kB] Get: 158 http://deb.debian.org/debian buster/main i386 junit4 all 4.12-8 [292 kB] Get: 159 http://deb.debian.org/debian buster/main i386 libactivation-java all 1.2.0-2 [84.7 kB] Get: 160 http://deb.debian.org/debian buster/main i386 libaopalliance-java all 20070526-6 [9048 B] Get: 161 http://deb.debian.org/debian buster/main i386 libapache-pom-java all 18-1 [4676 B] Get: 162 http://deb.debian.org/debian buster/main i386 libargs4j-java all 2.33-1 [139 kB] Get: 163 http://deb.debian.org/debian buster/main i386 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 164 http://deb.debian.org/debian buster/main i386 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 165 http://deb.debian.org/debian buster/main i386 libcdi-api-java all 1.2-2 [54.5 kB] Get: 166 http://deb.debian.org/debian buster/main i386 libjaxen-java all 1.1.6-4 [214 kB] Get: 167 http://deb.debian.org/debian buster/main i386 libdom4j-java all 2.1.1-2 [310 kB] Get: 168 http://deb.debian.org/debian buster/main i386 libcommons-parent-java all 43-1 [10.8 kB] Get: 169 http://deb.debian.org/debian buster/main i386 libcommons-io-java all 2.6-2 [213 kB] Get: 170 http://deb.debian.org/debian buster/main i386 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 171 http://deb.debian.org/debian buster/main i386 libcommons-cli-java all 1.4-1 [55.2 kB] Get: 172 http://deb.debian.org/debian buster/main i386 libcommons-lang3-java all 3.8-2 [478 kB] Get: 173 http://deb.debian.org/debian buster/main i386 libgeronimo-annotation-1.3-spec-java all 1.0-1 [10.6 kB] Get: 174 http://deb.debian.org/debian buster/main i386 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 175 http://deb.debian.org/debian buster/main i386 libguava-java all 19.0-1 [2028 kB] Get: 176 http://deb.debian.org/debian buster/main i386 libguice-java all 4.2.1-1 [962 kB] Get: 177 http://deb.debian.org/debian buster/main i386 libmaven-parent-java all 31-2 [5100 B] Get: 178 http://deb.debian.org/debian buster/main i386 libplexus-utils2-java all 3.1.1-1 [249 kB] Get: 179 http://deb.debian.org/debian buster/main i386 libwagon-provider-api-java all 3.3.1-2 [50.1 kB] Get: 180 http://deb.debian.org/debian buster/main i386 libmaven-resolver-java all 1.3.1-1 [549 kB] Get: 181 http://deb.debian.org/debian buster/main i386 libplexus-cipher-java all 1.7-3 [15.0 kB] Get: 182 http://deb.debian.org/debian buster/main i386 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 183 http://deb.debian.org/debian buster/main i386 libplexus-component-annotations-java all 1.7.1-7 [7536 B] Get: 184 http://deb.debian.org/debian buster/main i386 libplexus-interpolation-java all 1.25-1 [76.8 kB] Get: 185 http://deb.debian.org/debian buster/main i386 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 186 http://deb.debian.org/debian buster/main i386 libslf4j-java all 1.7.25-3 [143 kB] Get: 187 http://deb.debian.org/debian buster/main i386 libsisu-inject-java all 0.3.3-1 [347 kB] Get: 188 http://deb.debian.org/debian buster/main i386 libsisu-plexus-java all 0.3.3-3 [182 kB] Get: 189 http://deb.debian.org/debian buster/main i386 libmaven3-core-java all 3.6.0-1 [1465 kB] Get: 190 http://deb.debian.org/debian buster/main i386 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 191 http://deb.debian.org/debian buster/main i386 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 192 http://deb.debian.org/debian buster/main i386 libcommons-compress-java all 1.18-2 [530 kB] Get: 193 http://deb.debian.org/debian buster/main i386 libplexus-io-java all 3.1.1-1 [64.6 kB] Get: 194 http://deb.debian.org/debian buster/main i386 libsnappy1v5 i386 1.1.7-1 [18.0 kB] Get: 195 http://deb.debian.org/debian buster/main i386 libsnappy-jni i386 1.1.7.2-1 [7236 B] Get: 196 http://deb.debian.org/debian buster/main i386 libsnappy-java all 1.1.7.2-1 [73.7 kB] Get: 197 http://deb.debian.org/debian buster/main i386 libxz-java all 1.8-2 [141 kB] Get: 198 http://deb.debian.org/debian buster/main i386 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 199 http://deb.debian.org/debian buster/main i386 libsisu-guice-java all 4.2.0-1 [785 kB] Get: 200 http://deb.debian.org/debian buster/main i386 libsisu-ioc-java all 2.3.0-11 [492 kB] Get: 201 http://deb.debian.org/debian buster/main i386 libhttpcore-java all 4.4.11-1 [625 kB] Get: 202 http://deb.debian.org/debian buster/main i386 libcommons-codec-java all 1.11-1 [271 kB] Get: 203 http://deb.debian.org/debian buster/main i386 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 204 http://deb.debian.org/debian buster/main i386 libhttpclient-java all 4.5.7-1 [721 kB] Get: 205 http://deb.debian.org/debian buster/main i386 libjsoup-java all 1.10.2-2 [350 kB] Get: 206 http://deb.debian.org/debian buster/main i386 libwagon-http-java all 3.3.1-2 [50.5 kB] Get: 207 http://deb.debian.org/debian buster/main i386 libistack-commons-java all 3.0.6-3 [144 kB] Get: 208 http://deb.debian.org/debian buster/main i386 libcodemodel-java all 2.6+jaxb2.3.0.1-8 [163 kB] Get: 209 http://deb.debian.org/debian buster/main i386 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 210 http://deb.debian.org/debian buster/main i386 libcommons-pool-java all 1.6-3 [104 kB] Get: 211 http://deb.debian.org/debian buster/main i386 libcommons-dbcp-java all 1.4-6 [157 kB] Get: 212 http://deb.debian.org/debian buster/main i386 libcommons-math-java all 2.2-7 [928 kB] Get: 213 http://deb.debian.org/debian buster/main i386 libdtd-parser-java all 1.2~svn20110404-1 [62.5 kB] Get: 214 http://deb.debian.org/debian buster/main i386 libel-api-java all 3.0.0-2+deb10u1 [64.9 kB] Get: 215 http://deb.debian.org/debian buster/main i386 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 216 http://deb.debian.org/debian buster/main i386 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 217 http://deb.debian.org/debian buster/main i386 libstreambuffer-java all 1.5.4-1 [71.8 kB] Get: 218 http://deb.debian.org/debian buster/main i386 librelaxng-datatype-java all 1.0+ds1-3 [11.7 kB] Get: 219 http://deb.debian.org/debian buster/main i386 libxsom-java all 2.3.0.1-8 [396 kB] Get: 220 http://deb.debian.org/debian buster/main i386 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 221 http://deb.debian.org/debian buster/main i386 libgoogle-gson-java all 2.8.5-3 [225 kB] Get: 222 http://deb.debian.org/debian buster/main i386 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 223 http://deb.debian.org/debian buster/main i386 libjsp-api-java all 2.3.4-2+deb10u1 [53.7 kB] Get: 224 http://deb.debian.org/debian buster/main i386 libwebsocket-api-java all 1.1-1+deb10u1 [40.0 kB] Get: 225 http://deb.debian.org/debian buster/main i386 libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 226 http://deb.debian.org/debian buster/main i386 libhsqldb-java all 2.4.1-2 [1633 kB] Get: 227 http://deb.debian.org/debian buster/main i386 libitext5-java all 5.5.13-1 [2620 kB] Get: 228 http://deb.debian.org/debian buster/main i386 librngom-java all 2.3.0.1-8 [288 kB] Get: 229 http://deb.debian.org/debian buster/main i386 libtxw2-java all 2.3.0.1-8 [134 kB] Get: 230 http://deb.debian.org/debian buster/main i386 libxml-commons-resolver1.1-java all 1.2-9 [91.6 kB] Get: 231 http://deb.debian.org/debian buster/main i386 libjaxb-java all 2.3.0.1-8 [1966 kB] Get: 232 http://deb.debian.org/debian buster/main i386 libjaxp1.3-java all 1.3.05-5 [226 kB] Get: 233 http://deb.debian.org/debian buster/main i386 libjgraph-java all 5.12.4.2+dfsg-5 [205 kB] Get: 234 http://deb.debian.org/debian buster/main i386 libjgrapht0.8-java all 0.8.3-5 [214 kB] Get: 235 http://deb.debian.org/debian buster/main i386 libnaga-java all 3.0+svn80-2 [884 kB] Get: 236 http://deb.debian.org/debian buster/main i386 libjmol-java all 14.6.4+2016.11.05+dfsg1-4 [6393 kB] Get: 237 http://deb.debian.org/debian buster/main i386 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 238 http://deb.debian.org/debian buster/main i386 liblightcouch-java all 0.0.6-1 [63.7 kB] Get: 239 http://deb.debian.org/debian buster/main i386 liblog4j2-java all 2.11.1-2 [1721 kB] Get: 240 http://deb.debian.org/debian buster/main i386 libnetx-java all 0.5-4 [138 kB] Get: 241 http://deb.debian.org/debian buster/main i386 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 242 http://deb.debian.org/debian buster/main i386 libxmlunit-java all 1.6-1 [95.5 kB] Get: 243 http://deb.debian.org/debian buster/main i386 rdfind i386 1.4.1-1 [43.0 kB] Fetched 412 MB in 7s (59.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../1-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../2-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../3-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../4-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../5-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libssl1.1:i386. Preparing to unpack .../6-libssl1.1_1.1.1d-0+deb10u3_i386.deb ... Unpacking libssl1.1:i386 (1.1.1d-0+deb10u3) ... Selecting previously unselected package libpython3.7-minimal:i386. Preparing to unpack .../7-libpython3.7-minimal_3.7.3-2+deb10u1_i386.deb ... Unpacking libpython3.7-minimal:i386 (3.7.3-2+deb10u1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../8-libexpat1_2.2.6-2+deb10u1_i386.deb ... Unpacking libexpat1:i386 (2.2.6-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../9-python3.7-minimal_3.7.3-2+deb10u1_i386.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u1) ... Setting up libssl1.1:i386 (1.1.1d-0+deb10u3) ... Setting up libpython3.7-minimal:i386 (3.7.3-2+deb10u1) ... Setting up libexpat1:i386 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20129 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.3-1_i386.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libmpdec2:i386. Preparing to unpack .../2-libmpdec2_2.4.2-2_i386.deb ... Unpacking libmpdec2:i386 (2.4.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:i386. Preparing to unpack .../4-libreadline7_7.0-5_i386.deb ... Unpacking libreadline7:i386 (7.0-5) ... Selecting previously unselected package libpython3.7-stdlib:i386. Preparing to unpack .../5-libpython3.7-stdlib_3.7.3-2+deb10u1_i386.deb ... Unpacking libpython3.7-stdlib:i386 (3.7.3-2+deb10u1) ... Selecting previously unselected package python3.7. Preparing to unpack .../6-python3.7_3.7.3-2+deb10u1_i386.deb ... Unpacking python3.7 (3.7.3-2+deb10u1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../7-libpython3-stdlib_3.7.3-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20590 files and directories currently installed.) Preparing to unpack .../000-python3_3.7.3-1_i386.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../004-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../007-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../008-openssl_1.1.1d-0+deb10u3_i386.deb ... Unpacking openssl (1.1.1d-0+deb10u3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../009-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) ... Selecting previously unselected package libnspr4:i386. Preparing to unpack .../010-libnspr4_2%3a4.20-1_i386.deb ... Unpacking libnspr4:i386 (2:4.20-1) ... Selecting previously unselected package libnss3:i386. Preparing to unpack .../011-libnss3_2%3a3.42.1-1+deb10u2_i386.deb ... Unpacking libnss3:i386 (2:3.42.1-1+deb10u2) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../012-ca-certificates-java_20190405_all.deb ... Unpacking ca-certificates-java (20190405) ... Selecting previously unselected package java-common. Preparing to unpack .../013-java-common_0.71_all.deb ... Unpacking java-common (0.71) ... Selecting previously unselected package libavahi-common-data:i386. Preparing to unpack .../014-libavahi-common-data_0.7-4+b1_i386.deb ... Unpacking libavahi-common-data:i386 (0.7-4+b1) ... Selecting previously unselected package libavahi-common3:i386. Preparing to unpack .../015-libavahi-common3_0.7-4+b1_i386.deb ... Unpacking libavahi-common3:i386 (0.7-4+b1) ... Selecting previously unselected package libdbus-1-3:i386. Preparing to unpack .../016-libdbus-1-3_1.12.16-1_i386.deb ... Unpacking libdbus-1-3:i386 (1.12.16-1) ... Selecting previously unselected package libavahi-client3:i386. Preparing to unpack .../017-libavahi-client3_0.7-4+b1_i386.deb ... Unpacking libavahi-client3:i386 (0.7-4+b1) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../018-libkeyutils1_1.6-6_i386.deb ... Unpacking libkeyutils1:i386 (1.6-6) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../019-libkrb5support0_1.17-3_i386.deb ... Unpacking libkrb5support0:i386 (1.17-3) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../020-libk5crypto3_1.17-3_i386.deb ... Unpacking libk5crypto3:i386 (1.17-3) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../021-libkrb5-3_1.17-3_i386.deb ... Unpacking libkrb5-3:i386 (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../022-libgssapi-krb5-2_1.17-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.17-3) ... Selecting previously unselected package libcups2:i386. Preparing to unpack .../023-libcups2_2.2.10-6+deb10u3_i386.deb ... Unpacking libcups2:i386 (2.2.10-6+deb10u3) ... Selecting previously unselected package liblcms2-2:i386. Preparing to unpack .../024-liblcms2-2_2.9-3_i386.deb ... Unpacking liblcms2-2:i386 (2.9-3) ... Selecting previously unselected package libjpeg62-turbo:i386. Preparing to unpack .../025-libjpeg62-turbo_1%3a1.5.2-2+b1_i386.deb ... Unpacking libjpeg62-turbo:i386 (1:1.5.2-2+b1) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../026-libpng16-16_1.6.36-6_i386.deb ... Unpacking libpng16-16:i386 (1.6.36-6) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../027-libfreetype6_2.9.1-3+deb10u1_i386.deb ... Unpacking libfreetype6:i386 (2.9.1-3+deb10u1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../028-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../029-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../030-libfontconfig1_2.13.1-2_i386.deb ... Unpacking libfontconfig1:i386 (2.13.1-2) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../031-libasound2-data_1.1.8-1_all.deb ... Unpacking libasound2-data (1.1.8-1) ... Selecting previously unselected package libasound2:i386. Preparing to unpack .../032-libasound2_1.1.8-1_i386.deb ... Unpacking libasound2:i386 (1.1.8-1) ... Selecting previously unselected package libpcsclite1:i386. Preparing to unpack .../033-libpcsclite1_1.8.24-1_i386.deb ... Unpacking libpcsclite1:i386 (1.8.24-1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../034-libxau6_1%3a1.0.8-1+b2_i386.deb ... Unpacking libxau6:i386 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../035-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../036-libxcb1_1.13.1-2_i386.deb ... Unpacking libxcb1:i386 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../037-libx11-data_2%3a1.6.7-1_all.deb ... Unpacking libx11-data (2:1.6.7-1) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../038-libx11-6_2%3a1.6.7-1_i386.deb ... Unpacking libx11-6:i386 (2:1.6.7-1) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../039-libxext6_2%3a1.3.3-1+b2_i386.deb ... Unpacking libxext6:i386 (2:1.3.3-1+b2) ... Selecting previously unselected package libxi6:i386. Preparing to unpack .../040-libxi6_2%3a1.7.9-1_i386.deb ... Unpacking libxi6:i386 (2:1.7.9-1) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../041-libxrender1_1%3a0.9.10-1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.10-1) ... Selecting previously unselected package lsb-base. Preparing to unpack .../042-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package x11-common. Preparing to unpack .../043-x11-common_1%3a7.7+19_all.deb ... Unpacking x11-common (1:7.7+19) ... Selecting previously unselected package libxtst6:i386. Preparing to unpack .../044-libxtst6_2%3a1.2.3-1_i386.deb ... Unpacking libxtst6:i386 (2:1.2.3-1) ... Selecting previously unselected package openjdk-11-jre-headless:i386. Preparing to unpack .../045-openjdk-11-jre-headless_11.0.6+10-1~deb10u1_i386.deb ... Unpacking openjdk-11-jre-headless:i386 (11.0.6+10-1~deb10u1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../046-default-jre-headless_2%3a1.11-71_i386.deb ... Unpacking default-jre-headless (2:1.11-71) ... Selecting previously unselected package ant. Preparing to unpack .../047-ant_1.10.5-2_all.deb ... Unpacking ant (1.10.5-2) ... Selecting previously unselected package ant-contrib. Preparing to unpack .../048-ant-contrib_1.0~b3+svn177-10_all.deb ... Unpacking ant-contrib (1.0~b3+svn177-10) ... Selecting previously unselected package ant-optional. Preparing to unpack .../049-ant-optional_1.10.5-2_all.deb ... Unpacking ant-optional (1.10.5-2) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../050-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../051-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../052-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../053-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../054-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../055-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../056-dctrl-tools_2.24-3_i386.deb ... Unpacking dctrl-tools (2.24-3) ... Selecting previously unselected package libtool. Preparing to unpack .../057-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../058-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../059-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../060-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../061-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../062-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../063-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../064-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../065-libicu63_63.1-6+deb10u1_i386.deb ... Unpacking libicu63:i386 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../066-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../067-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../068-libncurses6_6.1+20181013-2+deb10u2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../069-gettext_0.19.8.1-9_i386.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../070-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../071-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../072-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package openjdk-11-doc. Preparing to unpack .../073-openjdk-11-doc_11.0.6+10-1~deb10u1_all.deb ... Unpacking openjdk-11-doc (11.0.6+10-1~deb10u1) ... Selecting previously unselected package default-jdk-doc. Preparing to unpack .../074-default-jdk-doc_2%3a1.11-71_i386.deb ... Unpacking default-jdk-doc (2:1.11-71) ... Selecting previously unselected package openjdk-11-jdk-headless:i386. Preparing to unpack .../075-openjdk-11-jdk-headless_11.0.6+10-1~deb10u1_i386.deb ... Unpacking openjdk-11-jdk-headless:i386 (11.0.6+10-1~deb10u1) ... Selecting previously unselected package default-jdk-headless. Preparing to unpack .../076-default-jdk-headless_2%3a1.11-71_i386.deb ... Unpacking default-jdk-headless (2:1.11-71) ... Selecting previously unselected package libassuan0:i386. Preparing to unpack .../077-libassuan0_2.5.2-1_i386.deb ... Unpacking libassuan0:i386 (2.5.2-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../078-gpgconf_2.2.12-1+deb10u1_i386.deb ... Unpacking gpgconf (2.2.12-1+deb10u1) ... Selecting previously unselected package libksba8:i386. Preparing to unpack .../079-libksba8_1.3.5-2_i386.deb ... Unpacking libksba8:i386 (1.3.5-2) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../080-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../081-libsasl2-2_2.1.27+dfsg-1+deb10u1_i386.deb ... Unpacking libsasl2-2:i386 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../082-libldap-common_2.4.47+dfsg-3+deb10u2_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libldap-2.4-2:i386. Preparing to unpack .../083-libldap-2.4-2_2.4.47+dfsg-3+deb10u2_i386.deb ... Unpacking libldap-2.4-2:i386 (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libnpth0:i386. Preparing to unpack .../084-libnpth0_1.6-1_i386.deb ... Unpacking libnpth0:i386 (1.6-1) ... Selecting previously unselected package dirmngr. Preparing to unpack .../085-dirmngr_2.2.12-1+deb10u1_i386.deb ... Unpacking dirmngr (2.2.12-1+deb10u1) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../086-gnupg-l10n_2.2.12-1+deb10u1_all.deb ... Unpacking gnupg-l10n (2.2.12-1+deb10u1) ... Selecting previously unselected package gnupg-utils. Preparing to unpack .../087-gnupg-utils_2.2.12-1+deb10u1_i386.deb ... Unpacking gnupg-utils (2.2.12-1+deb10u1) ... Selecting previously unselected package gpg. Preparing to unpack .../088-gpg_2.2.12-1+deb10u1_i386.deb ... Unpacking gpg (2.2.12-1+deb10u1) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../089-pinentry-curses_1.1.0-2_i386.deb ... Unpacking pinentry-curses (1.1.0-2) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../090-gpg-agent_2.2.12-1+deb10u1_i386.deb ... Unpacking gpg-agent (2.2.12-1+deb10u1) ... Selecting previously unselected package gpg-wks-client. Preparing to unpack .../091-gpg-wks-client_2.2.12-1+deb10u1_i386.deb ... Unpacking gpg-wks-client (2.2.12-1+deb10u1) ... Selecting previously unselected package gpg-wks-server. Preparing to unpack .../092-gpg-wks-server_2.2.12-1+deb10u1_i386.deb ... Unpacking gpg-wks-server (2.2.12-1+deb10u1) ... Selecting previously unselected package gpgsm. Preparing to unpack .../093-gpgsm_2.2.12-1+deb10u1_i386.deb ... Unpacking gpgsm (2.2.12-1+deb10u1) ... Selecting previously unselected package gnupg. Preparing to unpack .../094-gnupg_2.2.12-1+deb10u1_all.deb ... Unpacking gnupg (2.2.12-1+deb10u1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../095-libfile-which-perl_1.23-1_all.deb ... Unpacking libfile-which-perl (1.23-1) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../096-libfile-homedir-perl_1.004-1_all.deb ... Unpacking libfile-homedir-perl (1.004-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../097-libio-pty-perl_1%3a1.08-1.1+b5_i386.deb ... Unpacking libio-pty-perl (1:1.08-1.1+b5) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../098-libipc-run-perl_20180523.0-1_all.deb ... Unpacking libipc-run-perl (20180523.0-1) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../099-libclass-method-modifiers-perl_2.12-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.12-1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../100-libsub-exporter-progressive-perl_0.001013-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-1) ... Selecting previously unselected package libdevel-globaldestruction-perl. Preparing to unpack .../101-libdevel-globaldestruction-perl_0.14-1_all.deb ... Unpacking libdevel-globaldestruction-perl (0.14-1) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../102-libb-hooks-op-check-perl_0.22-1+b1_i386.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../103-libdynaloader-functions-perl_0.003-1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../104-libdevel-callchecker-perl_0.008-1_i386.deb ... Unpacking libdevel-callchecker-perl (0.008-1) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../105-libparams-classify-perl_0.015-1+b1_i386.deb ... Unpacking libparams-classify-perl (0.015-1+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../106-libmodule-runtime-perl_0.016-1_all.deb ... Unpacking libmodule-runtime-perl (0.016-1) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../107-libimport-into-perl_1.002005-1_all.deb ... Unpacking libimport-into-perl (1.002005-1) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../108-librole-tiny-perl_2.000006-1_all.deb ... Unpacking librole-tiny-perl (2.000006-1) ... Selecting previously unselected package libstrictures-perl. Preparing to unpack .../109-libstrictures-perl_2.000005-1_all.deb ... Unpacking libstrictures-perl (2.000005-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../110-libsub-quote-perl_2.005001-1_all.deb ... Unpacking libsub-quote-perl (2.005001-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../111-libmoo-perl_2.003004-2_all.deb ... Unpacking libmoo-perl (2.003004-2) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../112-libencode-locale-perl_1.05-1_all.deb ... Unpacking libencode-locale-perl (1.05-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../113-libtimedate-perl_2.3000-2+deb10u1_all.deb ... Unpacking libtimedate-perl (2.3000-2+deb10u1) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../114-libhttp-date-perl_6.02-1_all.deb ... Unpacking libhttp-date-perl (6.02-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../115-libfile-listing-perl_6.04-1_all.deb ... Unpacking libfile-listing-perl (6.04-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../116-libhtml-tagset-perl_3.20-3_all.deb ... Unpacking libhtml-tagset-perl (3.20-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../117-liburi-perl_1.76-1_all.deb ... Unpacking liburi-perl (1.76-1) ... Selecting previously unselected package libhtml-parser-perl. Preparing to unpack .../118-libhtml-parser-perl_3.72-3+b3_i386.deb ... Unpacking libhtml-parser-perl (3.72-3+b3) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../119-libhtml-tree-perl_5.07-2_all.deb ... Unpacking libhtml-tree-perl (5.07-2) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../120-libio-html-perl_1.001-1_all.deb ... Unpacking libio-html-perl (1.001-1) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../121-liblwp-mediatypes-perl_6.02-1_all.deb ... Unpacking liblwp-mediatypes-perl (6.02-1) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../122-libhttp-message-perl_6.18-1_all.deb ... Unpacking libhttp-message-perl (6.18-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../123-libhttp-cookies-perl_6.04-1_all.deb ... Unpacking libhttp-cookies-perl (6.04-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../124-libhttp-negotiate-perl_6.01-1_all.deb ... Unpacking libhttp-negotiate-perl (6.01-1) ... Selecting previously unselected package perl-openssl-defaults:i386. Preparing to unpack .../125-perl-openssl-defaults_3_i386.deb ... Unpacking perl-openssl-defaults:i386 (3) ... Selecting previously unselected package libnet-ssleay-perl. Preparing to unpack .../126-libnet-ssleay-perl_1.85-2+b1_i386.deb ... Unpacking libnet-ssleay-perl (1.85-2+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../127-libio-socket-ssl-perl_2.060-3_all.deb ... Unpacking libio-socket-ssl-perl (2.060-3) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../128-libnet-http-perl_6.18-1_all.deb ... Unpacking libnet-http-perl (6.18-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../129-liblwp-protocol-https-perl_6.07-2_all.deb ... Unpacking liblwp-protocol-https-perl (6.07-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../130-libtry-tiny-perl_0.30-1_all.deb ... Unpacking libtry-tiny-perl (0.30-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../131-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../132-libwww-perl_6.36-2_all.deb ... Unpacking libwww-perl (6.36-2) ... Selecting previously unselected package patchutils. Preparing to unpack .../133-patchutils_0.3.4-2_i386.deb ... Unpacking patchutils (0.3.4-2) ... Selecting previously unselected package wdiff. Preparing to unpack .../134-wdiff_1.2.2-2+b1_i386.deb ... Unpacking wdiff (1.2.2-2+b1) ... Selecting previously unselected package devscripts. Preparing to unpack .../135-devscripts_2.19.5+deb10u1_i386.deb ... Unpacking devscripts (2.19.5+deb10u1) ... Selecting previously unselected package javahelper. Preparing to unpack .../136-javahelper_0.72.9_all.deb ... Unpacking javahelper (0.72.9) ... Selecting previously unselected package junit. Preparing to unpack .../137-junit_3.8.2-9_all.deb ... Unpacking junit (3.8.2-9) ... Selecting previously unselected package libhamcrest-java. Preparing to unpack .../138-libhamcrest-java_1.3-9_all.deb ... Unpacking libhamcrest-java (1.3-9) ... Selecting previously unselected package junit4. Preparing to unpack .../139-junit4_4.12-8_all.deb ... Unpacking junit4 (4.12-8) ... Selecting previously unselected package libactivation-java. Preparing to unpack .../140-libactivation-java_1.2.0-2_all.deb ... Unpacking libactivation-java (1.2.0-2) ... Selecting previously unselected package libaopalliance-java. Preparing to unpack .../141-libaopalliance-java_20070526-6_all.deb ... Unpacking libaopalliance-java (20070526-6) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../142-libapache-pom-java_18-1_all.deb ... Unpacking libapache-pom-java (18-1) ... Selecting previously unselected package libargs4j-java. Preparing to unpack .../143-libargs4j-java_2.33-1_all.deb ... Unpacking libargs4j-java (2.33-1) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../144-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ... Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java. Preparing to unpack .../145-libgeronimo-interceptor-3.0-spec-java_1.0.1-4_all.deb ... Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Selecting previously unselected package libcdi-api-java. Preparing to unpack .../146-libcdi-api-java_1.2-2_all.deb ... Unpacking libcdi-api-java (1.2-2) ... Selecting previously unselected package libjaxen-java. Preparing to unpack .../147-libjaxen-java_1.1.6-4_all.deb ... Unpacking libjaxen-java (1.1.6-4) ... Selecting previously unselected package libdom4j-java. Preparing to unpack .../148-libdom4j-java_2.1.1-2_all.deb ... Unpacking libdom4j-java (2.1.1-2) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../149-libcommons-parent-java_43-1_all.deb ... Unpacking libcommons-parent-java (43-1) ... Selecting previously unselected package libcommons-io-java. Preparing to unpack .../150-libcommons-io-java_2.6-2_all.deb ... Unpacking libcommons-io-java (2.6-2) ... Selecting previously unselected package libmaven-shared-utils-java. Preparing to unpack .../151-libmaven-shared-utils-java_3.3.0-1_all.deb ... Unpacking libmaven-shared-utils-java (3.3.0-1) ... Selecting previously unselected package libcommons-cli-java. Preparing to unpack .../152-libcommons-cli-java_1.4-1_all.deb ... Unpacking libcommons-cli-java (1.4-1) ... Selecting previously unselected package libcommons-lang3-java. Preparing to unpack .../153-libcommons-lang3-java_3.8-2_all.deb ... Unpacking libcommons-lang3-java (3.8-2) ... Selecting previously unselected package libgeronimo-annotation-1.3-spec-java. Preparing to unpack .../154-libgeronimo-annotation-1.3-spec-java_1.0-1_all.deb ... Unpacking libgeronimo-annotation-1.3-spec-java (1.0-1) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../155-libjsr305-java_0.1~+svn49-11_all.deb ... Unpacking libjsr305-java (0.1~+svn49-11) ... Selecting previously unselected package libguava-java. Preparing to unpack .../156-libguava-java_19.0-1_all.deb ... Unpacking libguava-java (19.0-1) ... Selecting previously unselected package libguice-java. Preparing to unpack .../157-libguice-java_4.2.1-1_all.deb ... Unpacking libguice-java (4.2.1-1) ... Selecting previously unselected package libmaven-parent-java. Preparing to unpack .../158-libmaven-parent-java_31-2_all.deb ... Unpacking libmaven-parent-java (31-2) ... Selecting previously unselected package libplexus-utils2-java. Preparing to unpack .../159-libplexus-utils2-java_3.1.1-1_all.deb ... Unpacking libplexus-utils2-java (3.1.1-1) ... Selecting previously unselected package libwagon-provider-api-java. Preparing to unpack .../160-libwagon-provider-api-java_3.3.1-2_all.deb ... Unpacking libwagon-provider-api-java (3.3.1-2) ... Selecting previously unselected package libmaven-resolver-java. Preparing to unpack .../161-libmaven-resolver-java_1.3.1-1_all.deb ... Unpacking libmaven-resolver-java (1.3.1-1) ... Selecting previously unselected package libplexus-cipher-java. Preparing to unpack .../162-libplexus-cipher-java_1.7-3_all.deb ... Unpacking libplexus-cipher-java (1.7-3) ... Selecting previously unselected package libplexus-classworlds-java. Preparing to unpack .../163-libplexus-classworlds-java_2.6.0-1_all.deb ... Unpacking libplexus-classworlds-java (2.6.0-1) ... Selecting previously unselected package libplexus-component-annotations-java. Preparing to unpack .../164-libplexus-component-annotations-java_1.7.1-7_all.deb ... Unpacking libplexus-component-annotations-java (1.7.1-7) ... Selecting previously unselected package libplexus-interpolation-java. Preparing to unpack .../165-libplexus-interpolation-java_1.25-1_all.deb ... Unpacking libplexus-interpolation-java (1.25-1) ... Selecting previously unselected package libplexus-sec-dispatcher-java. Preparing to unpack .../166-libplexus-sec-dispatcher-java_1.4-4_all.deb ... Unpacking libplexus-sec-dispatcher-java (1.4-4) ... Selecting previously unselected package libslf4j-java. Preparing to unpack .../167-libslf4j-java_1.7.25-3_all.deb ... Unpacking libslf4j-java (1.7.25-3) ... Selecting previously unselected package libsisu-inject-java. Preparing to unpack .../168-libsisu-inject-java_0.3.3-1_all.deb ... Unpacking libsisu-inject-java (0.3.3-1) ... Selecting previously unselected package libsisu-plexus-java. Preparing to unpack .../169-libsisu-plexus-java_0.3.3-3_all.deb ... Unpacking libsisu-plexus-java (0.3.3-3) ... Selecting previously unselected package libmaven3-core-java. Preparing to unpack .../170-libmaven3-core-java_3.6.0-1_all.deb ... Unpacking libmaven3-core-java (3.6.0-1) ... Selecting previously unselected package libmaven-shared-io-java. Preparing to unpack .../171-libmaven-shared-io-java_3.0.0-3_all.deb ... Unpacking libmaven-shared-io-java (3.0.0-3) ... Selecting previously unselected package libmaven-file-management-java. Preparing to unpack .../172-libmaven-file-management-java_3.0.0-1_all.deb ... Unpacking libmaven-file-management-java (3.0.0-1) ... Selecting previously unselected package libcommons-compress-java. Preparing to unpack .../173-libcommons-compress-java_1.18-2_all.deb ... Unpacking libcommons-compress-java (1.18-2) ... Selecting previously unselected package libplexus-io-java. Preparing to unpack .../174-libplexus-io-java_3.1.1-1_all.deb ... Unpacking libplexus-io-java (3.1.1-1) ... Selecting previously unselected package libsnappy1v5:i386. Preparing to unpack .../175-libsnappy1v5_1.1.7-1_i386.deb ... Unpacking libsnappy1v5:i386 (1.1.7-1) ... Selecting previously unselected package libsnappy-jni. Preparing to unpack .../176-libsnappy-jni_1.1.7.2-1_i386.deb ... Unpacking libsnappy-jni (1.1.7.2-1) ... Selecting previously unselected package libsnappy-java. Preparing to unpack .../177-libsnappy-java_1.1.7.2-1_all.deb ... Unpacking libsnappy-java (1.1.7.2-1) ... Selecting previously unselected package libxz-java. Preparing to unpack .../178-libxz-java_1.8-2_all.deb ... Unpacking libxz-java (1.8-2) ... Selecting previously unselected package libplexus-archiver-java. Preparing to unpack .../179-libplexus-archiver-java_3.6.0-2_all.deb ... Unpacking libplexus-archiver-java (3.6.0-2) ... Selecting previously unselected package libsisu-guice-java. Preparing to unpack .../180-libsisu-guice-java_4.2.0-1_all.deb ... Unpacking libsisu-guice-java (4.2.0-1) ... Selecting previously unselected package libsisu-ioc-java. Preparing to unpack .../181-libsisu-ioc-java_2.3.0-11_all.deb ... Unpacking libsisu-ioc-java (2.3.0-11) ... Selecting previously unselected package libhttpcore-java. Preparing to unpack .../182-libhttpcore-java_4.4.11-1_all.deb ... Unpacking libhttpcore-java (4.4.11-1) ... Selecting previously unselected package libcommons-codec-java. Preparing to unpack .../183-libcommons-codec-java_1.11-1_all.deb ... Unpacking libcommons-codec-java (1.11-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../184-libcommons-logging-java_1.2-2_all.deb ... Unpacking libcommons-logging-java (1.2-2) ... Selecting previously unselected package libhttpclient-java. Preparing to unpack .../185-libhttpclient-java_4.5.7-1_all.deb ... Unpacking libhttpclient-java (4.5.7-1) ... Selecting previously unselected package libjsoup-java. Preparing to unpack .../186-libjsoup-java_1.10.2-2_all.deb ... Unpacking libjsoup-java (1.10.2-2) ... Selecting previously unselected package libwagon-http-java. Preparing to unpack .../187-libwagon-http-java_3.3.1-2_all.deb ... Unpacking libwagon-http-java (3.3.1-2) ... Selecting previously unselected package libistack-commons-java. Preparing to unpack .../188-libistack-commons-java_3.0.6-3_all.deb ... Unpacking libistack-commons-java (3.0.6-3) ... Selecting previously unselected package libcodemodel-java. Preparing to unpack .../189-libcodemodel-java_2.6+jaxb2.3.0.1-8_all.deb ... Unpacking libcodemodel-java (2.6+jaxb2.3.0.1-8) ... Selecting previously unselected package libcommons-collections3-java. Preparing to unpack .../190-libcommons-collections3-java_3.2.2-2_all.deb ... Unpacking libcommons-collections3-java (3.2.2-2) ... Selecting previously unselected package libcommons-pool-java. Preparing to unpack .../191-libcommons-pool-java_1.6-3_all.deb ... Unpacking libcommons-pool-java (1.6-3) ... Selecting previously unselected package libcommons-dbcp-java. Preparing to unpack .../192-libcommons-dbcp-java_1.4-6_all.deb ... Unpacking libcommons-dbcp-java (1.4-6) ... Selecting previously unselected package libcommons-math-java. Preparing to unpack .../193-libcommons-math-java_2.2-7_all.deb ... Unpacking libcommons-math-java (2.2-7) ... Selecting previously unselected package libdtd-parser-java. Preparing to unpack .../194-libdtd-parser-java_1.2~svn20110404-1_all.deb ... Unpacking libdtd-parser-java (1.2~svn20110404-1) ... Selecting previously unselected package libel-api-java. Preparing to unpack .../195-libel-api-java_3.0.0-2+deb10u1_all.deb ... Unpacking libel-api-java (3.0.0-2+deb10u1) ... Selecting previously unselected package libjaxb-api-java. Preparing to unpack .../196-libjaxb-api-java_2.3.1-1_all.deb ... Unpacking libjaxb-api-java (2.3.1-1) ... Selecting previously unselected package libstax-ex-java. Preparing to unpack .../197-libstax-ex-java_1.7.8-3_all.deb ... Unpacking libstax-ex-java (1.7.8-3) ... Selecting previously unselected package libstreambuffer-java. Preparing to unpack .../198-libstreambuffer-java_1.5.4-1_all.deb ... Unpacking libstreambuffer-java (1.5.4-1) ... Selecting previously unselected package librelaxng-datatype-java. Preparing to unpack .../199-librelaxng-datatype-java_1.0+ds1-3_all.deb ... Unpacking librelaxng-datatype-java (1.0+ds1-3) ... Selecting previously unselected package libxsom-java. Preparing to unpack .../200-libxsom-java_2.3.0.1-8_all.deb ... Unpacking libxsom-java (2.3.0.1-8) ... Selecting previously unselected package libfastinfoset-java. Preparing to unpack .../201-libfastinfoset-java_1.2.12-3_all.deb ... Unpacking libfastinfoset-java (1.2.12-3) ... Selecting previously unselected package libgoogle-gson-java. Preparing to unpack .../202-libgoogle-gson-java_2.8.5-3_all.deb ... Unpacking libgoogle-gson-java (2.8.5-3) ... Selecting previously unselected package libservlet-api-java. Preparing to unpack .../203-libservlet-api-java_4.0.1-2_all.deb ... Unpacking libservlet-api-java (4.0.1-2) ... Selecting previously unselected package libjsp-api-java. Preparing to unpack .../204-libjsp-api-java_2.3.4-2+deb10u1_all.deb ... Unpacking libjsp-api-java (2.3.4-2+deb10u1) ... Selecting previously unselected package libwebsocket-api-java. Preparing to unpack .../205-libwebsocket-api-java_1.1-1+deb10u1_all.deb ... Unpacking libwebsocket-api-java (1.1-1+deb10u1) ... Selecting previously unselected package libservlet3.1-java. Preparing to unpack .../206-libservlet3.1-java_1%3a4.0.1-2_all.deb ... Unpacking libservlet3.1-java (1:4.0.1-2) ... Selecting previously unselected package libhsqldb-java. Preparing to unpack .../207-libhsqldb-java_2.4.1-2_all.deb ... Unpacking libhsqldb-java (2.4.1-2) ... Selecting previously unselected package libitext5-java. Preparing to unpack .../208-libitext5-java_5.5.13-1_all.deb ... Unpacking libitext5-java (5.5.13-1) ... Selecting previously unselected package librngom-java. Preparing to unpack .../209-librngom-java_2.3.0.1-8_all.deb ... Unpacking librngom-java (2.3.0.1-8) ... Selecting previously unselected package libtxw2-java. Preparing to unpack .../210-libtxw2-java_2.3.0.1-8_all.deb ... Unpacking libtxw2-java (2.3.0.1-8) ... Selecting previously unselected package libxml-commons-resolver1.1-java. Preparing to unpack .../211-libxml-commons-resolver1.1-java_1.2-9_all.deb ... Unpacking libxml-commons-resolver1.1-java (1.2-9) ... Selecting previously unselected package libjaxb-java. Preparing to unpack .../212-libjaxb-java_2.3.0.1-8_all.deb ... Unpacking libjaxb-java (2.3.0.1-8) ... Selecting previously unselected package libjaxp1.3-java. Preparing to unpack .../213-libjaxp1.3-java_1.3.05-5_all.deb ... Unpacking libjaxp1.3-java (1.3.05-5) ... Selecting previously unselected package libjgraph-java. Preparing to unpack .../214-libjgraph-java_5.12.4.2+dfsg-5_all.deb ... Unpacking libjgraph-java (5.12.4.2+dfsg-5) ... Selecting previously unselected package libjgrapht0.8-java. Preparing to unpack .../215-libjgrapht0.8-java_0.8.3-5_all.deb ... Unpacking libjgrapht0.8-java (0.8.3-5) ... Selecting previously unselected package libnaga-java. Preparing to unpack .../216-libnaga-java_3.0+svn80-2_all.deb ... Unpacking libnaga-java (3.0+svn80-2) ... Selecting previously unselected package libjmol-java. Preparing to unpack .../217-libjmol-java_14.6.4+2016.11.05+dfsg1-4_all.deb ... Unpacking libjmol-java (14.6.4+2016.11.05+dfsg1-4) ... Selecting previously unselected package libjson-simple-java. Preparing to unpack .../218-libjson-simple-java_2.3.0-1_all.deb ... Unpacking libjson-simple-java (2.3.0-1) ... Selecting previously unselected package liblightcouch-java. Preparing to unpack .../219-liblightcouch-java_0.0.6-1_all.deb ... Unpacking liblightcouch-java (0.0.6-1) ... Selecting previously unselected package liblog4j2-java. Preparing to unpack .../220-liblog4j2-java_2.11.1-2_all.deb ... Unpacking liblog4j2-java (2.11.1-2) ... Selecting previously unselected package libnetx-java. Preparing to unpack .../221-libnetx-java_0.5-4_all.deb ... Unpacking libnetx-java (0.5-4) ... Selecting previously unselected package libvecmath-java. Preparing to unpack .../222-libvecmath-java_1.5.2-7_all.deb ... Unpacking libvecmath-java (1.5.2-7) ... Selecting previously unselected package libxmlunit-java. Preparing to unpack .../223-libxmlunit-java_1.6-1_all.deb ... Unpacking libxmlunit-java (1.6-1) ... Selecting previously unselected package rdfind. Preparing to unpack .../224-rdfind_1.4.1-1_i386.deb ... Unpacking rdfind (1.4.1-1) ... Setting up libksba8:i386 (1.3.5-2) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up liblcms2-2:i386 (2.9-3) ... Setting up libdtd-parser-java (1.2~svn20110404-1) ... Setting up wdiff (1.2.2-2+b1) ... Setting up lsb-base (10.2019051400) ... Setting up libslf4j-java (1.7.25-3) ... Setting up libfile-which-perl (1.23-1) ... Setting up libxau6:i386 (1:1.0.8-1+b2) ... Setting up libplexus-utils2-java (3.1.1-1) ... Setting up libkeyutils1:i386 (1.6-6) ... Setting up libplexus-classworlds-java (2.6.0-1) ... Setting up mime-support (3.62) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up java-common (0.71) ... Setting up libnetx-java (0.5-4) ... Setting up libdynaloader-functions-perl (0.003-1) ... Setting up libclass-method-modifiers-perl (2.12-1) ... Setting up libaopalliance-java (20070526-6) ... Setting up libcommons-cli-java (1.4-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libvecmath-java (1.5.2-7) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:i386 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libgoogle-gson-java (2.8.5-3) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up rdfind (1.4.1-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.30-1) ... Setting up libmagic1:i386 (1:5.35-4+deb10u1) ... Setting up perl-openssl-defaults:i386 (3) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libel-api-java (3.0.0-2+deb10u1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libplexus-component-annotations-java (1.7.1-7) ... Setting up libnpth0:i386 (1.6-1) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libjson-simple-java (2.3.0-1) ... Setting up libassuan0:i386 (2.5.2-1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libicu63:i386 (63.1-6+deb10u1) ... Setting up libplexus-cipher-java (1.7-3) ... Setting up libsnappy1v5:i386 (1.1.7-1) ... Setting up libkrb5support0:i386 (1.17-3) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-1+deb10u1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.0-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-2) ... Setting up libasound2-data (1.1.8-1) ... Setting up patchutils (0.3.4-2) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:i386 (1:1.5.2-2+b1) ... Setting up junit (3.8.2-9) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libnspr4:i386 (2:4.20-1) ... Setting up gnupg-l10n (2.2.12-1+deb10u1) ... Setting up libapache-pom-java (18-1) ... Setting up libavahi-common-data:i386 (0.7-4+b1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:i386 (1.12.16-1) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libwebsocket-api-java (1.1-1+deb10u1) ... Setting up libplexus-interpolation-java (1.25-1) ... Setting up libpng16-16:i386 (1.6.36-6) ... Setting up libitext5-java (5.5.13-1) ... Setting up libxml-commons-resolver1.1-java (1.2-9) ... Setting up libxz-java (1.8-2) ... Setting up openjdk-11-doc (11.0.6+10-1~deb10u1) ... Setting up libio-html-perl (1.001-1) ... Setting up libcommons-pool-java (1.6-3) ... Setting up autopoint (0.19.8.1-9) ... Setting up libb-hooks-op-check-perl (0.22-1+b1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libpcsclite1:i386 (1.8.24-1) ... Setting up libk5crypto3:i386 (1.17-3) ... Setting up libjgraph-java (5.12.4.2+dfsg-5) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (1.3-9) ... Setting up libjsp-api-java (2.3.4-2+deb10u1) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-1+deb10u1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libtimedate-perl (2.3000-2+deb10u1) ... Setting up sensible-utils (0.0.12) ... Setting up libjsoup-java (1.10.2-2) ... Setting up libcommons-math-java (2.2-7) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libasound2:i386 (1.1.8-1) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.000006-1) ... Setting up libplexus-sec-dispatcher-java (1.4-4) ... Setting up libdevel-globaldestruction-perl (0.14-1) ... Setting up netbase (5.6) ... Setting up libstrictures-perl (2.000005-1) ... Setting up libsub-quote-perl (2.005001-1) ... Setting up libkrb5-3:i386 (1.17-3) ... Setting up libmpdec2:i386 (2.4.2-2) ... Setting up libhttpcore-java (4.4.11-1) ... Setting up libjaxp1.3-java (1.3.05-5) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up librelaxng-datatype-java (1.0+ds1-3) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libcdi-api-java (1.2-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libsnappy-jni (1.1.7.2-1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up liburi-perl (1.76-1) ... Setting up libargs4j-java (2.33-1) ... Setting up dctrl-tools (2.24-3) ... Setting up libservlet3.1-java (1:4.0.1-2) ... Setting up libreadline7:i386 (7.0-5) ... Setting up gnupg-utils (2.2.12-1+deb10u1) ... Setting up libnaga-java (3.0+svn80-2) ... Setting up libnet-ssleay-perl (1.85-2+b1) ... Setting up pinentry-curses (1.1.0-2) ... Setting up libdom4j-java (2.1.1-2) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libwagon-provider-api-java (3.3.1-2) ... Setting up libcommons-dbcp-java (1.4-6) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:i386 (3.7.3-2+deb10u1) ... Setting up libxcb1:i386 (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:i386 (0.7-4+b1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:i386 (2.4.47+dfsg-3+deb10u2) ... Setting up libnet-http-perl (6.18-1) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:i386 (2:3.42.1-1+deb10u2) ... Setting up default-jdk-doc (2:1.11-71) ... Setting up libdevel-callchecker-perl (0.008-1) ... Setting up libxmlunit-java (1.6-1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libmaven-resolver-java (1.3.1-1) ... Setting up libfreetype6:i386 (2.9.1-3+deb10u1) ... Setting up libguava-java (19.0-1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libstreambuffer-java (1.5.4-1) ... Setting up libgssapi-krb5-2:i386 (1.17-3) ... Setting up libcroco3:i386 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libcommons-lang3-java (3.8-2) ... Setting up autoconf (2.69-11) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up librngom-java (2.3.0.1-8) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libsisu-guice-java (4.2.0-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.12-1+deb10u1) ... Setting up libx11-6:i386 (2:1.6.7-1) ... Setting up libsnappy-java (1.1.7.2-1) ... Setting up libxsom-java (2.3.0.1-8) ... Setting up libcommons-codec-java (1.11-1) ... Setting up libavahi-client3:i386 (0.7-4+b1) ... Setting up libio-socket-ssl-perl (2.060-3) ... Setting up gpg (2.2.12-1+deb10u1) ... Setting up libjmol-java (14.6.4+2016.11.05+dfsg1-4) ... Setting up libpython3-stdlib:i386 (3.7.3-1) ... Setting up libhttp-message-perl (6.18-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u1) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up gettext (0.19.8.1-9) ... Setting up gpg-agent (2.2.12-1+deb10u1) ... Setting up libxrender1:i386 (1:0.9.10-1) ... Setting up libcommons-compress-java (1.18-2) ... Setting up libhttp-cookies-perl (6.04-1) ... Setting up libcommons-io-java (2.6-2) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b1) ... Setting up gpgsm (2.2.12-1+deb10u1) ... Setting up libxext6:i386 (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:i386 (2.2.10-6+deb10u3) ... Setting up libhttpclient-java (4.5.7-1) ... Setting up liblightcouch-java (0.0.6-1) ... Setting up libwagon-http-java (3.3.1-2) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfontconfig1:i386 (2.13.1-2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libplexus-io-java (3.1.1-1) ... Setting up libxi6:i386 (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:i386 (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:i386 (11.0.6+10-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode OpenJDK Client VM warning: Ignoring option PermSize; support was removed in 8.0 Setting up openjdk-11-jdk-headless:i386 (11.0.6+10-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/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:COMODO_RSA_Certification_Authority.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:ISRG_Root_X1.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Secure_Global_CA.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:EC-ACC.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Certigna.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:AffirmTrust_Premium.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:AddTrust_External_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:TrustCor_ECA-1.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:ACCVRAIZ1.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Taiwan_GRCA.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:SecureTrust_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Izenpe.com.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem done. Setting up junit4 (4.12-8) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up ant-contrib (1.0~b3+svn177-10) ... Setting up debhelper (12.1.1) ... Setting up ant-optional (1.10.5-2) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up javahelper (0.72.9) ... Setting up libistack-commons-java (3.0.6-3) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-8) ... Setting up libtxw2-java (2.3.0.1-8) ... Setting up libjaxb-java (2.3.0.1-8) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" 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 i386 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: 1 second 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: 6 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: 2 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: 1 second 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: 1 second 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: 1 second 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: 1 second 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: 1 second 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: 5 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 136 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 49 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 23 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 2 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL Total time: 1 second 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: 1 second cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 13 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/ronn/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/data/sequence/package-info.class [copy] Copying 11 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL Total time: 1 second 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: 1 second 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: 1 second 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: 2 seconds # make doc rm -rf biojavadoc mkdir biojavadoc cp -r biojava-*/src biojavadoc/ sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml cd biojavadoc && ant javadocs Buildfile: /build/biojava4-live-4.2.12+dfsg/biojavadoc/build.xml javadocs: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/javadoc [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/doc/biojava [javadoc] Generating Javadoc [javadoc] Debian build on Java 9+ detected: Adding the --ignore-source-errors option [javadoc] Javadoc execution [javadoc] Loading source files for package org.biojava.nbio.aaproperties... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.profeat... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.xml... [javadoc] Loading source files for package org.biojava.nbio.alignment... [javadoc] Loading source files for package org.biojava.nbio.alignment.io... [javadoc] Loading source files for package org.biojava.nbio.alignment.routines... [javadoc] Loading source files for package org.biojava.nbio.alignment.template... [javadoc] Loading source files for package org.biojava.nbio.core.alignment... [javadoc] Loading source files for package org.biojava.nbio.core.alignment.matrices... [javadoc] Loading source files for package org.biojava.nbio.core.alignment.template... [javadoc] Loading source files for package org.biojava.nbio.core.exceptions... [javadoc] Loading source files for package org.biojava.nbio.core.search.io... [javadoc] Loading source files for package org.biojava.nbio.core.search.io.blast... [javadoc] Loading source files for package org.biojava.nbio.core.sequence... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.compound... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.edits... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.features... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io.util... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.loader... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.location... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.location.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.storage... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.transcription... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.views... [javadoc] Loading source files for package org.biojava.nbio.core.util... [javadoc] Loading source files for package org.biojava.nbio.data.sequence... [javadoc] Loading source files for package org.biojava.nbio.genome... [javadoc] Loading source files for package org.biojava.nbio.genome.homology... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.cytoband... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.geneid... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.genename... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.gff... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.twobit... [javadoc] Loading source files for package org.biojava.nbio.genome.query... [javadoc] Loading source files for package org.biojava.nbio.genome.uniprot... [javadoc] Loading source files for package org.biojava.nbio.genome.util... [javadoc] Loading source files for package org.biojava.nbio.ontology... [javadoc] Loading source files for package org.biojava.nbio.ontology.io... [javadoc] Loading source files for package org.biojava.nbio.ontology.obo... [javadoc] Loading source files for package org.biojava.nbio.ontology.utils... [javadoc] Loading source files for package org.biojava.nbio.phosphosite... [javadoc] Loading source files for package org.biojava.nbio.phylo... [javadoc] Loading source files for package org.biojava.nbio.proteincomparisontool... [javadoc] Loading source files for package org.biojava.nbio.protmod... [javadoc] Loading source files for package org.biojava.nbio.protmod.io... [javadoc] Loading source files for package org.biojava.nbio.protmod.structure... [javadoc] Loading source files for package org.biojava.nbio.ronn... [javadoc] Loading source files for package org.biojava.nbio.sequencing.io.fastq... [javadoc] Loading source files for package org.biojava.nbio.structure... [javadoc] Loading source files for package org.biojava.nbio.structure.align... [javadoc] Loading source files for package org.biojava.nbio.structure.align.ce... [javadoc] Loading source files for package org.biojava.nbio.structure.align.client... [javadoc] Loading source files for package org.biojava.nbio.structure.align.events... [javadoc] Loading source files for package org.biojava.nbio.structure.align.fatcat... [javadoc] Loading source files for package org.biojava.nbio.structure.align.fatcat.calc... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.jmol... [javadoc] Loading source files for package org.biojava.nbio.structure.align.helper... [javadoc] Loading source files for package org.biojava.nbio.structure.align.model... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple.mc... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple.util... [javadoc] Loading source files for package org.biojava.nbio.structure.align.pairwise... [javadoc] Loading source files for package org.biojava.nbio.structure.align.seq... [javadoc] Loading source files for package org.biojava.nbio.structure.align.util... [javadoc] Loading source files for package org.biojava.nbio.structure.align.webstart... [javadoc] Loading source files for package org.biojava.nbio.structure.align.xml... [javadoc] Loading source files for package org.biojava.nbio.structure.asa... [javadoc] Loading source files for package org.biojava.nbio.structure.cath... [javadoc] Loading source files for package org.biojava.nbio.structure.contact... [javadoc] Loading source files for package org.biojava.nbio.structure.domain... [javadoc] Loading source files for package org.biojava.nbio.structure.domain.pdp... [javadoc] Loading source files for package org.biojava.nbio.structure.ecod... [javadoc] Loading source files for package org.biojava.nbio.structure.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.events... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.util... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.util.color... [javadoc] Loading source files for package org.biojava.nbio.structure.io... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif.chem... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif.model... [javadoc] Loading source files for package org.biojava.nbio.structure.io.sifts... [javadoc] Loading source files for package org.biojava.nbio.structure.io.util... [javadoc] Loading source files for package org.biojava.nbio.structure.jama... [javadoc] Loading source files for package org.biojava.nbio.structure.math... [javadoc] Loading source files for package org.biojava.nbio.structure.quaternary... [javadoc] Loading source files for package org.biojava.nbio.structure.quaternary.io... [javadoc] Loading source files for package org.biojava.nbio.structure.rcsb... [javadoc] Loading source files for package org.biojava.nbio.structure.scop... [javadoc] Loading source files for package org.biojava.nbio.structure.scop.server... [javadoc] Loading source files for package org.biojava.nbio.structure.secstruc... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.analysis... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.core... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.geometry... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.internal... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.misc... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.utils... [javadoc] Loading source files for package org.biojava.nbio.structure.validation... [javadoc] Loading source files for package org.biojava.nbio.structure.xtal... [javadoc] Loading source files for package org.biojava.nbio.structure.xtal.io... [javadoc] Loading source files for package org.biojava.nbio.survival.cox... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.comparators... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.matrix... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.stats... [javadoc] Loading source files for package org.biojava.nbio.survival.data... [javadoc] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure... [javadoc] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... [javadoc] Loading source files for package org.biojava.nbio.ws.alignment... [javadoc] Loading source files for package org.biojava.nbio.ws.alignment.qblast... [javadoc] Loading source files for package org.biojava.nbio.ws.hmmer... [javadoc] Loading source files for package org.forester.analysis... [javadoc] Loading source files for package org.forester.application... [javadoc] Loading source files for package org.forester.applications... [javadoc] Loading source files for package org.forester.archaeopteryx... [javadoc] Loading source files for package org.forester.archaeopteryx.phylogeny.data... [javadoc] Loading source files for package org.forester.archaeopteryx.tools... [javadoc] Loading source files for package org.forester.archaeopteryx.webservices... [javadoc] Loading source files for package org.forester.datastructures... [javadoc] Loading source files for package org.forester.development... [javadoc] Loading source files for package org.forester.evoinference... [javadoc] Loading source files for package org.forester.evoinference.distance... [javadoc] Loading source files for package org.forester.evoinference.matrix.character... [javadoc] Loading source files for package org.forester.evoinference.matrix.distance... [javadoc] Loading source files for package org.forester.evoinference.parsimony... [javadoc] Loading source files for package org.forester.evoinference.tools... [javadoc] Loading source files for package org.forester.go... [javadoc] Loading source files for package org.forester.go.etc... [javadoc] Loading source files for package org.forester.io.parsers... [javadoc] Loading source files for package org.forester.io.parsers.nexus... [javadoc] Loading source files for package org.forester.io.parsers.nhx... [javadoc] Loading source files for package org.forester.io.parsers.phyloxml... [javadoc] Loading source files for package org.forester.io.parsers.phyloxml.data... [javadoc] Loading source files for package org.forester.io.parsers.tol... [javadoc] Loading source files for package org.forester.io.parsers.util... [javadoc] Loading source files for package org.forester.io.writers... [javadoc] Loading source files for package org.forester.msa... [javadoc] Loading source files for package org.forester.msa_compactor... [javadoc] Loading source files for package org.forester.pccx... [javadoc] Loading source files for package org.forester.phylogeny... [javadoc] Loading source files for package org.forester.phylogeny.data... [javadoc] Loading source files for package org.forester.phylogeny.factories... [javadoc] Loading source files for package org.forester.phylogeny.iterators... [javadoc] Loading source files for package org.forester.protein... [javadoc] Loading source files for package org.forester.rio... [javadoc] Loading source files for package org.forester.sdi... [javadoc] Loading source files for package org.forester.sequence... [javadoc] Loading source files for package org.forester.species... [javadoc] Loading source files for package org.forester.surfacing... [javadoc] Loading source files for package org.forester.test... [javadoc] Loading source files for package org.forester.test.examples... [javadoc] Loading source files for package org.forester.tools... [javadoc] Loading source files for package org.forester.util... [javadoc] Loading source files for package org.forester.ws.hmmer... [javadoc] Loading source files for package org.forester.ws.seqdb... [javadoc] Loading source files for package org.forester.ws.wabi... [javadoc] Loading source files for package org.jcolorbrewer... [javadoc] Loading source files for package org.jcolorbrewer.ui... [javadoc] Constructing Javadoc information... [javadoc] javadoc: error - Error fetching URL: http://java.sun.com/j2se/1.6.0/docs/api/ [javadoc] Standard Doclet version 11.0.6 [javadoc] Building tree for all the packages and classes... [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag < [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag > [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag < [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag > [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:38: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:39: warning - Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java:44: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java:163: warning - @param argument "dbReference" is not a parameter name. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning - invalid usage of tag < [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning - @param argument "cutsPerSection" is not a parameter name. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning - @param argument "cutsPerSection" is not a parameter name. [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning - invalid usage of tag < [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:105: warning - invalid usage of tag > [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:130: warning - invalid usage of tag > [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning - Tag @link: reference not found: Aligner [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning - invalid usage of tag < [javadoc] Building index for all the packages and classes... [javadoc] Building index for all classes... [javadoc] Building index for all classes... [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/help-doc.html... [javadoc] 1 error [javadoc] 100 warnings BUILD SUCCESSFUL Total time: 12 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 11.0.6 [junit] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.055 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.055 sec [junit] [junit] Testcase: testGetIndexOf took 0.018 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetNumGaps took 0 sec [junit] Testcase: testGetStart took 0 sec [junit] Testcase: testGetSequenceIndexAt took 0.001 sec [junit] Testcase: testGetAccession took 0 sec [junit] Testcase: testToString took 0.001 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 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.001 sec [junit] Testcase: testGetOriginalSequence took 0.001 sec [junit] Testcase: testGetCompoundAt took 0 sec [junit] Testcase: testGetLength took 0 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 0.001 sec [junit] Testcase: testIterator took 0 sec [junit] Testcase: testGetSequenceAsString took 0 sec [junit] Testcase: testGetLastIndexOf took 0 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.001 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: 0.096 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.096 sec [junit] [junit] Testcase: testGetIndexOf took 0.033 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequenceInt took 0.001 sec [junit] Testcase: testToStringInt took 0.005 sec [junit] Testcase: testToString took 0.001 sec [junit] Testcase: testToStringFormatted took 0.009 sec [junit] Testcase: testSimpleProfile took 0 sec [junit] Testcase: testGetSize took 0 sec [junit] Testcase: testGetAlignedSequenceS took 0 sec [junit] Testcase: testGetAlignedSequences took 0 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 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.001 sec [junit] Testcase: testGetCompoundAtIntInt took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0 sec [junit] Testcase: testGetLength took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 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 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetCompoundsAt took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 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 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 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0 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: 0.069 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.032 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0 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 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumIdenticals took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAt took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumSimilars took 0 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: 0.055 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetAlignment took 0.027 sec [junit] Testcase: testHashCode took 0 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: 0.164 sec [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.164 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] Aug 21, 2021 11:34:00 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Aug 21, 2021 11:34:00 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 0.092 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 0.052 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0.002 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: 3 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 22 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 10 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 45 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec [junit] [junit] Testcase: testGetQuery took 0.027 sec [junit] Testcase: testGetScore took 0.011 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0 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: 0.057 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec [junit] [junit] Testcase: testGetQuery took 0.028 sec [junit] Testcase: testGetScore took 0.011 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0 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: 0.104 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 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 0.061 sec [junit] Testcase: testToString took 0.002 sec [junit] Testcase: testGetScoreMatrix took 0.002 sec [junit] Testcase: testGetRoot took 0.014 sec [junit] Testcase: testGetSequences took 0.001 sec [junit] Testcase: testGetDistanceMatrix took 0.001 sec [junit] Testcase: testGetAllPairsScores took 0.001 sec [junit] Testcase: testIterator took 0.001 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: 0.059 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec [junit] [junit] Testcase: shouldAllowZeroLengthMatches took 0.046 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: 0.205 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.028 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.011 sec [junit] Testcase: should_align_middle_anchor took 0.01 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0 sec [junit] Testcase: testNeedlemanWunsch took 0 sec [junit] Testcase: should_align_all_anchored took 0 sec [junit] Testcase: testGetScoreMatrix took 0 sec [junit] Testcase: testGetPair took 0.001 sec [junit] Testcase: should_align_multiple_anchors took 0 sec [junit] Testcase: testAnchoredDNAAlignment took 0.002 sec [junit] Testcase: testGetProfile took 0 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: should_align_ending_anchor took 0 sec [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec [junit] Testcase: testComplex took 0.004 sec [junit] Testcase: testGetScoreMatrixAsString took 0.007 sec [junit] Testcase: should_align_starting_anchor took 0.001 sec [junit] Testcase: anchors_should_not_change_score took 0 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0 sec [junit] Testcase: testIntOverflowBug took 0.117 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: 0.018 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] [junit] Testcase: testOpenPenalty took 0.002 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: 0.059 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec [junit] [junit] Testcase: testGetQuery took 0.042 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testSimpleProfilePair took 0.002 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: 0.084 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.04 sec [junit] Testcase: testGetGapPenalty took 0.001 sec [junit] Testcase: testGetComputationTime took 0.001 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0.002 sec [junit] Testcase: testGetPair took 0.003 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.011 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0 sec [junit] Testcase: testSimpleProfileProfileAligner took 0 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 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: 0.057 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.003 sec [junit] Testcase: testSetDescription took 0.01 sec [junit] Testcase: testToString took 0.015 sec [junit] Testcase: testCaseEquivalence took 0.001 sec [junit] Testcase: test took 0.005 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.004 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.001 sec [junit] Testcase: testSetName took 0.002 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.001 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: 0.075 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.027 sec [junit] Testcase: testGetGapPenalty took 0.001 sec [junit] Testcase: testGetComputationTime took 0.011 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.002 sec [junit] Testcase: testSmithWaterman took 0.001 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.014 sec [junit] Testcase: testSetStoringScoreMatrix took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0 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: 0.022 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.001 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.001 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 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 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: 0.068 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec [junit] [junit] Testcase: testGetComputationTime took 0.038 sec [junit] Testcase: testGuanUberbacher took 0.001 sec [junit] Testcase: testGetScore took 0 sec [junit] Testcase: testGetPair took 0.002 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: should_align_shorter_target took 0.009 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: 5 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 9 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 7 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [copy] Copying 32 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.354 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.354 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 0.294 sec [junit] Testcase: testExample1 took 0.014 sec [junit] Testcase: testExample2 took 0.004 sec [junit] Testcase: testExample3 took 0.013 sec [junit] Testcase: testExample1WithCSV took 0.01 sec [junit] Testcase: testWithCases took 0.002 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: 0.314 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 sec [junit] [junit] Testcase: shortExample1 took 0.014 sec [junit] Testcase: shortExample2 took 0.243 sec [junit] Testcase: shortExample3 took 0.029 sec [junit] Testcase: shortExample4 took 0.001 sec [junit] Testcase: shortExample5 took 0.002 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: 0.37 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.37 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 0.296 sec [junit] Testcase: testExample1 took 0.009 sec [junit] Testcase: testExample2 took 0.005 sec [junit] Testcase: testExample3 took 0.005 sec [junit] Testcase: testExample1WithCSV took 0.005 sec [junit] Testcase: testWithCases took 0.004 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: 0.504 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 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 0.016 sec [junit] Testcase: testMolecularWeightXMLSingleFile took 0.264 sec [junit] Testcase: testEnrichment took 0.006 sec [junit] Testcase: testApliphaticIndex took 0.001 sec [junit] Testcase: testMolecularWeightXMLNull took 0.003 sec [junit] Testcase: testApliphaticIndexNull took 0 sec [junit] Testcase: testIsoelectricPointExpasy took 0.001 sec [junit] Testcase: testAbsorbanceNull took 0 sec [junit] Testcase: testIsoelectricPointNull took 0 sec [junit] Testcase: testAverageHydropathy took 0 sec [junit] Testcase: testExtinctionCoefficient took 0.001 sec [junit] Testcase: testAAComposition took 0 sec [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.017 sec [junit] Testcase: testMolecularWeight took 0.001 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.001 sec [junit] Testcase: testNetChargeNull took 0.001 sec [junit] Testcase: testExtinctionCoefficientNull took 0 sec [junit] Testcase: testNetCharge took 0.064 sec [junit] Testcase: testEnrichmentNull took 0 sec [junit] Testcase: testInstabilityIndexNull took 0 sec [junit] Testcase: testAverageHydropathyNull took 0 sec [junit] Testcase: testMolecularWeightXML took 0.025 sec [junit] Testcase: testInstabilityIndex took 0 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: 0.015 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] [junit] Testcase: testFake took 0 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: 0.025 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 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: 0.447 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.447 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 0.198 sec [junit] Testcase: readWithIDXml took 0.076 sec [junit] Testcase: readMinXml took 0.027 sec [junit] Testcase: readAdvancedXml took 0.013 sec [junit] Testcase: generateXml took 0.015 sec [junit] Testcase: readXml took 0.023 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: 0.343 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 sec [junit] [junit] Testcase: generateSchema took 0.203 sec [junit] Testcase: generateXml took 0.033 sec [junit] Testcase: readXml took 0.085 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: 0.026 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] [junit] Testcase: testFake took 0 sec BUILD SUCCESSFUL Total time: 6 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 2 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 2 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 8 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes test: [echo] Using java version 11.0.6 BUILD SUCCESSFUL Total time: 1 second # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 14 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 74 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 19 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec [junit] [junit] Testcase: testConvert took 0.061 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 0.003 sec [junit] Testcase: testBuildNullDescription took 0 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 0.001 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 sec [junit] Testcase: testBuildNullQuality took 0 sec [junit] Testcase: testBuildMultiple took 0 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: 0.016 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] [junit] Testcase: testImmutable took 0.002 sec [junit] Testcase: testBuilder took 0.002 sec [junit] Testcase: testVariant took 0 sec [junit] Testcase: testQuality took 0.002 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0 sec [junit] Testcase: testDescription took 0 sec [junit] Testcase: testConstructor took 0 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: 0.068 sec [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec [junit] [junit] Testcase: testErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.001 sec [junit] Testcase: testConvertNullVariant took 0 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.031 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0.001 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 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 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.001 sec [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0 sec [junit] Testcase: testQualityScores took 0.003 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: 0.112 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec [junit] [junit] Testcase: testParseFastqVariant took 0.002 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec [junit] Testcase: testIsSanger took 0.002 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec [junit] Testcase: testIsSolexa took 0 sec [junit] Testcase: testIsIllumina took 0 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: 0.338 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec [junit] [junit] Testcase: testFullRangeAsIllumina took 0.021 sec [junit] Testcase: testWrappingAsIllumina took 0.002 sec [junit] Testcase: testValidateDescription took 0.005 sec [junit] Testcase: testValidateRepeatDescription took 0.002 sec [junit] Testcase: testMiscDnaAsIllumina took 0.001 sec [junit] Testcase: testMiscRnaAsIllumina took 0.001 sec [junit] Testcase: testLongReadsAsIllumina took 0.002 sec [junit] Testcase: testParseNullReadable took 0 sec [junit] Testcase: testReadRoundTripSingleFile took 0.011 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.011 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 sec [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0 sec [junit] Testcase: testWrappedQuality took 0 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: 0.027 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.004 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec [junit] Testcase: testWriteFileIterable took 0.01 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.SangerFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec [junit] [junit] Testcase: testMiscRnaAsSanger took 0.021 sec [junit] Testcase: testFullRangeAsSanger took 0.002 sec [junit] Testcase: testWrappingOriginal took 0.001 sec [junit] Testcase: testLongReadsOriginal took 0.002 sec [junit] Testcase: testMiscDnaOriginal took 0.001 sec [junit] Testcase: testMiscRnaOriginal took 0.001 sec [junit] Testcase: testValidateDescription took 0.004 sec [junit] Testcase: testValidateRepeatDescription took 0.001 sec [junit] Testcase: testFullRangeOriginal took 0.001 sec [junit] Testcase: testWrappingAsSanger took 0.001 sec [junit] Testcase: testLongReadsAsSanger took 0.001 sec [junit] Testcase: testMiscDnaAsSanger took 0.001 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.011 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.009 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 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 sec [junit] Testcase: testReadEmptyURL took 0 sec [junit] Testcase: testReadRoundTripMultipleFile took 0 sec [junit] Testcase: testWrappedQuality took 0 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: 0.028 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec [junit] [junit] Testcase: testConvertNotSangerVariant took 0.005 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec [junit] Testcase: testWriteFileIterable took 0.009 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.001 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: 0.074 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec [junit] [junit] Testcase: testMiscRnaAsSolexa took 0.021 sec [junit] Testcase: testFullRangeAsSolexa took 0.002 sec [junit] Testcase: testValidateDescription took 0.005 sec [junit] Testcase: testValidateRepeatDescription took 0.001 sec [junit] Testcase: testWrappingAsSolexa took 0.001 sec [junit] Testcase: testLongReadsAsSolexa took 0.002 sec [junit] Testcase: testMiscDnaAsSolexa took 0.001 sec [junit] Testcase: testParseNullReadable took 0 sec [junit] Testcase: testReadRoundTripSingleFile took 0.011 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.01 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 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 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0 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: 0.028 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec [junit] [junit] Testcase: testConvertNotSolexaVariant took 0.005 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec [junit] Testcase: testWriteFileIterable took 0.01 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0.001 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: 0.011 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] [junit] Testcase: testStreamNullVariant took 0.001 sec [junit] Testcase: testStreamNullListener took 0.001 sec [junit] Testcase: testStreamNullReadable took 0.001 sec BUILD SUCCESSFUL Total time: 5 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure #cd biojava-protein-disorder && ant test # Requires remote access and tmp directory write access #cd biojava-structure && ant test cd biojava-structure-gui && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 5 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/src/test/resources does not exist. [copy] Copying 141 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes test: [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] [junit] Testcase: testMe took 0 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: 0.008 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 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: 0.018 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] [junit] Testcase: testGetColor took 0.002 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec [junit] Testcase: testGetSelection took 0.002 sec [junit] Testcase: testRepaint took 0.001 sec [junit] Testcase: testSetSelection took 0 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec [junit] Testcase: testSetStyle took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] [junit] Testcase: testStructureLoad took 0 sec BUILD SUCCESSFUL Total time: 2 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 2 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 5 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 36 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes test: [echo] Using java version 11.0.6 BUILD SUCCESSFUL Total time: 1 second 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 10334 files. Now scanning "debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java", found 1874 files. Now have 12208 files in total. Removed 0 files due to nonunique device and inode. Total size is 323318469 bytes or 308 MiB Removed 7242 files due to unique sizes from list.4966 files left. Now eliminating candidates based on first bytes:removed 804 files from list.4162 files left. Now eliminating candidates based on last bytes:removed 19 files from list.4143 files left. Now eliminating candidates based on sha1 checksum:removed 4103 files from list.40 files left. It seems like you have 40 files that are not unique Totally, 1 MiB can be reduced. Now making results file results.txt Now making symbolic links. creating Failed moving /usr/share/doc/openjdk-11-jre-headless/api/jquery/external/jquery/jquery.js to a temporary file Failed to make symlink /usr/share/doc/openjdk-11-jre-headless/api/jquery/external/jquery/jquery.js to /usr/share/doc/openjdk-11-jre-headless/api/jquery/jquery-3.3.1.js Making 20 links. make[1]: 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-java-doc' in '../libbiojava4-java-doc_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-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava4-live_4.2.12+dfsg-2_i386.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/61522 and its subdirectories I: Current time: Sat Aug 21 23:34:42 -12 2021 I: pbuilder-time-stamp: 1629632082 Mon Jul 20 05:11:45 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build12-i386.debian.net. Mon Jul 20 05:11:45 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build12-i386.debian.net. Mon Jul 20 05:33:42 UTC 2020 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. Mon Jul 20 05:33:42 UTC 2020 I: biojava4-live_4.2.12+dfsg-2_i386.changes: Format: 1.8 Date: Fri, 18 Jan 2019 11:47:46 -0800 Source: biojava4-live Binary: libbiojava4-java libbiojava4-java-doc libbiojava4.0-java Architecture: all Version: 4.2.12+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libbiojava4-java - Java API to biological data and applications (default version) libbiojava4-java-doc - [Biology] Documentation for BioJava libbiojava4.0-java - Java API to biological data and applications (version 4) Changes: biojava4-live (4.2.12+dfsg-2) unstable; urgency=medium . * Team upload. * Switch to libnetx-java from icedtea-netx and downgrade to a Suggests. It is only needed by biojava-structure-gui for one operation, which is done by reflection. * Replace embedded copy of JavaScript libraries with symlinks to the dependency of default-jdk-doc. * debian/copyright: added explanation for repacked upstream tarball Checksums-Sha1: 65cc89d46b1a10c1957eb012fa1860ea7abd3afe 12336 biojava4-live_4.2.12+dfsg-2_i386.buildinfo 0bccdd11d0532b431c2a4260d30b6398b11632bb 1979196 libbiojava4-java-doc_4.2.12+dfsg-2_all.deb 2facbbcceb7ad839b738f8845bc310de7f166d5a 4572 libbiojava4-java_4.2.12+dfsg-2_all.deb e0166871d31a682852c574e7d541701a0f96b77d 5451992 libbiojava4.0-java_4.2.12+dfsg-2_all.deb Checksums-Sha256: 7ce0a61f0f189fb61085a473546a3f36bdf26d2dc6e987a49a26d51500c292ed 12336 biojava4-live_4.2.12+dfsg-2_i386.buildinfo 612aafc45130d92b865dd720dc99a9aeeef35246968cba17ae31eb54ae5282d1 1979196 libbiojava4-java-doc_4.2.12+dfsg-2_all.deb ac35e88e466f6bd4b9df54764a03c2c4233db5e9fb68a53ac4fe4c3b74173fef 4572 libbiojava4-java_4.2.12+dfsg-2_all.deb 1f61a61d607fc7db64ff0052cc2f58e7ceb075b469783ba93820c18dd758f9de 5451992 libbiojava4.0-java_4.2.12+dfsg-2_all.deb Files: 590c91fed431566050d49a5931075204 12336 java optional biojava4-live_4.2.12+dfsg-2_i386.buildinfo 9da3b629aa27498a13ee3aedc7a61779 1979196 doc optional libbiojava4-java-doc_4.2.12+dfsg-2_all.deb 56d7cd07abc8ad1b7fa0e9b0252286ab 4572 java optional libbiojava4-java_4.2.12+dfsg-2_all.deb 3d2e645dd5b5c23ebe626bc1bbb2b183 5451992 java optional libbiojava4.0-java_4.2.12+dfsg-2_all.deb Mon Jul 20 05:33:44 UTC 2020 I: diffoscope 152 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/biojava4-live_4.2.12+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/biojava4-live_4.2.12+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/biojava4-live_4.2.12+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/b1/biojava4-live_4.2.12+dfsg-2_i386.changes /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/b2/biojava4-live_4.2.12+dfsg-2_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.378s) 0.378s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.133s) 0.133s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 20 05:33:45 UTC 2020 I: diffoscope 152 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 20 05:33:45 UTC 2020 I: biojava4-live from buster built successfully and reproducibly on i386. Mon Jul 20 05:33:47 UTC 2020 I: Submitting .buildinfo files to external archives: Mon Jul 20 05:33:47 UTC 2020 I: Submitting 16K b1/biojava4-live_4.2.12+dfsg-2_i386.buildinfo.asc Mon Jul 20 05:33:48 UTC 2020 I: Submitting 16K b2/biojava4-live_4.2.12+dfsg-2_i386.buildinfo.asc Mon Jul 20 05:33:50 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 20 05:33:50 UTC 2020 I: Done submitting .buildinfo files. Mon Jul 20 05:33:50 UTC 2020 I: Removing signed biojava4-live_4.2.12+dfsg-2_i386.buildinfo.asc files: removed './b1/biojava4-live_4.2.12+dfsg-2_i386.buildinfo.asc' removed './b2/biojava4-live_4.2.12+dfsg-2_i386.buildinfo.asc'