Thu Jun 24 15:24:14 UTC 2021 I: starting to build biojava4-live/bullseye/i386 on jenkins on '2021-06-24 15:23' Thu Jun 24 15:24:14 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/10769/console.log Thu Jun 24 15:24:14 UTC 2021 I: Downloading source for bullseye/biojava4-live=4.2.12+dfsg-3.1 --2021-06-24 15:24:14-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/biojava4-live/biojava4-live_4.2.12+dfsg-3.1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2489 (2.4K) Saving to: ‘biojava4-live_4.2.12+dfsg-3.1.dsc’ 0K .. 100% 127M=0s 2021-06-24 15:24:14 (127 MB/s) - ‘biojava4-live_4.2.12+dfsg-3.1.dsc’ saved [2489/2489] Thu Jun 24 15:24:14 UTC 2021 I: biojava4-live_4.2.12+dfsg-3.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: biojava4-live Binary: libbiojava4.0-java, libbiojava4-java, libbiojava4-java-doc Architecture: all Version: 4.2.12+dfsg-3.1 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 5d32fa4d241ce1c0f2c8ebaff3cf670c65ea715b 15776 biojava4-live_4.2.12+dfsg-3.1.debian.tar.xz Checksums-Sha256: 63ea99c016b4bbb87a62c9cb05d0dbc352845851c200b676821037d76c6021c7 12178028 biojava4-live_4.2.12+dfsg.orig.tar.xz d6201590a2ef181415f9f6b9cde4a78f3a01052ab380a0cb8832f73d6e905f49 15776 biojava4-live_4.2.12+dfsg-3.1.debian.tar.xz Files: c66ea841163dc423be3713cf937cef2a 12178028 biojava4-live_4.2.12+dfsg.orig.tar.xz eef7582b381a1ac71c95e27de7bd1026 15776 biojava4-live_4.2.12+dfsg-3.1.debian.tar.xz Dgit: 0eaf5ecd2622558d28031b92506b0d1972f0a2e2 debian archive/debian/4.2.12+dfsg-3.1 https://git.dgit.debian.org/biojava4-live -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEWLZtSHNr6TsFLeZynFyZ6wW9dQoFAl8MthQACgkQnFyZ6wW9 dQrZiwf/c8S9dGMqQ2nrnWlkwoNYcwRkX70sTcgjgBFFPXLlJ19PIlKO+e2ZsUYA v2+rq05QQOZM3+ODqnyCZL1B6vnAtst+HBKpc+wbuYQbwvLo3da3XPjZTVcd5EoK qdCDzL4W4nwT2jQb05dJVfABKNXmgLCNTvydvlODL/Bgjeiwg9m5NIPXRIWkWe7v eobfPatPOl/eRzJJLimDDG9iwVHE/6pwIib1d8e69uFuuncR/XMsYtcTh3J8pucU K9rXR5Q5n2yFJ1U4DXYvYZQ7rSa5NFTZdRjWOVT5Q648Kzof9LalsIpY2Gt4Zf0v LBuoHth125kdqUMZwf94JvivgcX7+w== =wvhS -----END PGP SIGNATURE----- Thu Jun 24 15:24:14 UTC 2021 I: Checking whether the package is not for us Thu Jun 24 15:24:14 UTC 2021 I: Starting 1st build on remote node ionos2-i386.debian.net. Thu Jun 24 15:24:14 UTC 2021 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Thu Jun 24 15:45:27 UTC 2021 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 24 03:24:25 -12 2021 I: pbuilder-time-stamp: 1624548265 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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-3.1.dsc] I: copying [./biojava4-live_4.2.12+dfsg.orig.tar.xz] I: copying [./biojava4-live_4.2.12+dfsg-3.1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.AyA3MCMj/trustedkeys.kbx': General error gpgv: Signature made Mon Jul 13 07:29:24 2020 -12 gpgv: using RSA key 58B66D48736BE93B052DE6729C5C99EB05BD750A gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biojava4-live_4.2.12+dfsg-3.1.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-3.1.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/30254/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,-fixfilepath parallel=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='61870b0fc77f49988794f2016fb43393' 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='30254' 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.6lQib42wHB/pbuilderrc_ACI6 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.6lQib42wHB/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-3.1.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://78.137.99.97:3128' I: uname -a Linux ionos2-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-1 (2021-06-10) i686 GNU/Linux I: ls -l /bin total 5780 -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jun 23 21:25 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/30254/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 ... 19675 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} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk-doc{a} default-jdk-headless{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} 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} libbrotli1{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} libcups2{a} libdbus-1-3{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libelf1{a} libencode-locale-perl{a} libexpat1{a} libfastinfoset-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} 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} libgraphite2-3{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{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} libicu67{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} libjgraph-java{a} libjgrapht0.8-java{a} libjmol-java{a} libjpeg62-turbo{a} libjson-simple-java{a} libjsoup-java{a} libjsr305-java{a} libksba8{a} liblcms2-2{a} libldap-2.4-2{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} libmongodb-java{a} libmoo-perl{a} libmpdec3{a} libnaga-java{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} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librelaxng-datatype-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libservlet-api-java{a} libsigsegv2{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libstax-ex-java{a} libstreambuffer-java{a} libstrictures-perl{a} libsub-override-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} libwww-perl{a} libwww-robotrules-perl{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxmlunit-java{a} libxsom-java{a} libxz-java{a} m4{a} man-db{a} media-types{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} python3.9{a} python3.9-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} ucf{a} wdiff{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus debian-keyring dput dput-ng dupload equivs libarchive-cpio-perl libclass-xsaccessor-perl libclone-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libjansi-java libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libsub-name-perl licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg shared-mime-info strace unzip wget xdg-user-dirs 0 packages upgraded, 221 newly installed, 0 to remove and 0 not upgraded. Need to get 421 MB of archives. After unpacking 941 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 netbase all 6.3 [19.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 openssl i386 1.1.1k-1 [860 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 ca-certificates all 20210119 [158 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libnspr4 i386 2:4.29-1 [122 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libnss3 i386 2:3.61-1 [1384 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 ca-certificates-java all 20190909 [15.7 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 java-common all 0.72 [14.5 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libavahi-common-data i386 0.8-5 [123 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libavahi-common3 i386 0.8-5 [60.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libdbus-1-3 i386 1.12.20-2 [232 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libavahi-client3 i386 0.8-5 [64.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libcups2 i386 2.3.3op2-3+deb11u1 [366 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 liblcms2-2 i386 2.12~rc1-2 [161 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libasound2 i386 1.2.4-1.1 [379 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libharfbuzz0b i386 2.7.4-1 [1490 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libpcsclite1 i386 1.9.1-1 [61.7 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 openjdk-11-jre-headless i386 11.0.11+9-1 [36.9 MB] Get: 51 http://deb.debian.org/debian bullseye/main i386 default-jre-headless i386 2:1.11-72 [10.9 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 ant all 1.10.9-4 [2118 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 ant-optional all 1.10.9-4 [381 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 dctrl-tools i386 2.24-3 [105 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 openjdk-11-doc all 11.0.11+9-1 [13.5 MB] Get: 78 http://deb.debian.org/debian bullseye/main i386 default-jdk-doc i386 2:1.11-72 [11.0 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 openjdk-11-jdk-headless i386 11.0.11+9-1 [287 MB] Get: 80 http://deb.debian.org/debian bullseye/main i386 default-jdk-headless i386 2:1.11-72 [1100 B] Get: 81 http://deb.debian.org/debian bullseye/main i386 libassuan0 i386 2.5.3-7.1 [52.7 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 gpgconf i386 2.2.27-2 [555 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libksba8 i386 1.5.0-3 [131 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libnpth0 i386 1.6-3 [19.1 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 dirmngr i386 2.2.27-2 [790 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 gnupg-l10n all 2.2.27-2 [1084 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 gnupg-utils i386 2.2.27-2 [952 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 gpg i386 2.2.27-2 [969 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 pinentry-curses i386 1.1.0-4 [66.5 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 gpg-agent i386 2.2.27-2 [690 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 gpg-wks-client i386 2.2.27-2 [535 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 gpg-wks-server i386 2.2.27-2 [526 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 gpgsm i386 2.2.27-2 [666 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 gnupg all 2.2.27-2 [825 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libfile-dirlist-perl all 0.05-2 [7444 B] Get: 99 http://deb.debian.org/debian bullseye/main i386 libfile-which-perl all 1.23-1 [16.6 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 libfile-homedir-perl all 1.006-1 [43.8 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 libfile-touch-perl all 0.11-1 [9254 B] Get: 102 http://deb.debian.org/debian bullseye/main i386 libio-pty-perl i386 1:1.15-2 [37.8 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 libipc-run-perl all 20200505.0-1 [102 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 libb-hooks-op-check-perl i386 0.22-1+b3 [11.4 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 107 http://deb.debian.org/debian bullseye/main i386 libdevel-callchecker-perl i386 0.008-1+b2 [15.9 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 libparams-classify-perl i386 0.015-1+b3 [26.4 kB] Get: 109 http://deb.debian.org/debian bullseye/main i386 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 libstrictures-perl all 2.000006-1 [18.6 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 libsub-quote-perl all 2.006006-1 [21.0 kB] Get: 114 http://deb.debian.org/debian bullseye/main i386 libmoo-perl all 2.004004-1 [59.9 kB] Get: 115 http://deb.debian.org/debian bullseye/main i386 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 libhttp-date-perl all 6.05-1 [10.4 kB] Get: 118 http://deb.debian.org/debian bullseye/main i386 libfile-listing-perl all 6.14-1 [12.4 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 liburi-perl all 5.08-1 [90.6 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 libhtml-parser-perl i386 3.75-1+b1 [106 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 libhtml-tree-perl all 5.07-2 [213 kB] Get: 123 http://deb.debian.org/debian bullseye/main i386 libio-html-perl all 1.004-2 [16.1 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 libhttp-message-perl all 6.28-1 [79.6 kB] Get: 126 http://deb.debian.org/debian bullseye/main i386 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 128 http://deb.debian.org/debian bullseye/main i386 perl-openssl-defaults i386 5 [7360 B] Get: 129 http://deb.debian.org/debian bullseye/main i386 libnet-ssleay-perl i386 1.88-3+b1 [328 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 libio-socket-ssl-perl all 2.069-1 [215 kB] Get: 131 http://deb.debian.org/debian bullseye/main i386 libnet-http-perl all 6.20-1 [25.1 kB] Get: 132 http://deb.debian.org/debian bullseye/main i386 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 133 http://deb.debian.org/debian bullseye/main i386 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 134 http://deb.debian.org/debian bullseye/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 135 http://deb.debian.org/debian bullseye/main i386 libwww-perl all 6.52-1 [192 kB] Get: 136 http://deb.debian.org/debian bullseye/main i386 patchutils i386 0.4.2-1 [79.6 kB] Get: 137 http://deb.debian.org/debian bullseye/main i386 wdiff i386 1.2.2-2+b1 [123 kB] Get: 138 http://deb.debian.org/debian bullseye/main i386 devscripts i386 2.21.2 [1092 kB] Get: 139 http://deb.debian.org/debian bullseye/main i386 javahelper all 0.78 [97.2 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 junit all 3.8.2-9 [110 kB] Get: 141 http://deb.debian.org/debian bullseye/main i386 libhamcrest-java all 1.3-9 [388 kB] Get: 142 http://deb.debian.org/debian bullseye/main i386 junit4 all 4.13.1-2 [347 kB] Get: 143 http://deb.debian.org/debian bullseye/main i386 libactivation-java all 1.2.0-2 [84.7 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 libaopalliance-java all 20070526-6 [9048 B] Get: 145 http://deb.debian.org/debian bullseye/main i386 libapache-pom-java all 18-1 [4676 B] Get: 146 http://deb.debian.org/debian bullseye/main i386 libargs4j-java all 2.33-1.1 [137 kB] Get: 147 http://deb.debian.org/debian bullseye/main i386 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 148 http://deb.debian.org/debian bullseye/main i386 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 149 http://deb.debian.org/debian bullseye/main i386 libcdi-api-java all 1.2-3 [54.3 kB] Get: 150 http://deb.debian.org/debian bullseye/main i386 libjaxen-java all 1.1.6-4 [214 kB] Get: 151 http://deb.debian.org/debian bullseye/main i386 libdom4j-java all 2.1.3-1 [310 kB] Get: 152 http://deb.debian.org/debian bullseye/main i386 libcommons-parent-java all 43-1 [10.8 kB] Get: 153 http://deb.debian.org/debian bullseye/main i386 libcommons-io-java all 2.8.0-1 [279 kB] Get: 154 http://deb.debian.org/debian bullseye/main i386 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 155 http://deb.debian.org/debian bullseye/main i386 libcommons-cli-java all 1.4-2 [57.3 kB] Get: 156 http://deb.debian.org/debian bullseye/main i386 libcommons-lang3-java all 3.11-1 [550 kB] Get: 157 http://deb.debian.org/debian bullseye/main i386 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 158 http://deb.debian.org/debian bullseye/main i386 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 159 http://deb.debian.org/debian bullseye/main i386 libguava-java all 29.0-6 [2419 kB] Get: 160 http://deb.debian.org/debian bullseye/main i386 libguice-java all 4.2.3-2 [1435 kB] Get: 161 http://deb.debian.org/debian bullseye/main i386 libmaven-parent-java all 31-2 [5100 B] Get: 162 http://deb.debian.org/debian bullseye/main i386 libplexus-utils2-java all 3.3.0-1 [250 kB] Get: 163 http://deb.debian.org/debian bullseye/main i386 libwagon-provider-api-java all 3.3.4-1 [50.2 kB] Get: 164 http://deb.debian.org/debian bullseye/main i386 libmaven-resolver-java all 1.4.2-3 [556 kB] Get: 165 http://deb.debian.org/debian bullseye/main i386 libplexus-cipher-java all 1.8-2 [15.0 kB] Get: 166 http://deb.debian.org/debian bullseye/main i386 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 167 http://deb.debian.org/debian bullseye/main i386 libplexus-component-annotations-java all 2.1.0-1 [7620 B] Get: 168 http://deb.debian.org/debian bullseye/main i386 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 169 http://deb.debian.org/debian bullseye/main i386 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 170 http://deb.debian.org/debian bullseye/main i386 libslf4j-java all 1.7.30-1 [144 kB] Get: 171 http://deb.debian.org/debian bullseye/main i386 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 172 http://deb.debian.org/debian bullseye/main i386 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 173 http://deb.debian.org/debian bullseye/main i386 libmaven3-core-java all 3.6.3-5 [1538 kB] Get: 174 http://deb.debian.org/debian bullseye/main i386 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 175 http://deb.debian.org/debian bullseye/main i386 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 176 http://deb.debian.org/debian bullseye/main i386 libcommons-compress-java all 1.20-1 [574 kB] Get: 177 http://deb.debian.org/debian bullseye/main i386 libplexus-io-java all 3.2.0-1.1 [65.0 kB] Get: 178 http://deb.debian.org/debian bullseye/main i386 libsnappy1v5 i386 1.1.8-1 [19.0 kB] Get: 179 http://deb.debian.org/debian bullseye/main i386 libsnappy-jni i386 1.1.8.3-1 [7384 B] Get: 180 http://deb.debian.org/debian bullseye/main i386 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 181 http://deb.debian.org/debian bullseye/main i386 libxz-java all 1.8-2 [141 kB] Get: 182 http://deb.debian.org/debian bullseye/main i386 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 183 http://deb.debian.org/debian bullseye/main i386 libhttpcore-java all 4.4.14-1 [631 kB] Get: 184 http://deb.debian.org/debian bullseye/main i386 libcommons-codec-java all 1.15-1 [292 kB] Get: 185 http://deb.debian.org/debian bullseye/main i386 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 186 http://deb.debian.org/debian bullseye/main i386 libhttpclient-java all 4.5.13-2 [1233 kB] Get: 187 http://deb.debian.org/debian bullseye/main i386 libjsoup-java all 1.10.2-2 [350 kB] Get: 188 http://deb.debian.org/debian bullseye/main i386 libwagon-http-java all 3.3.4-1 [53.9 kB] Get: 189 http://deb.debian.org/debian bullseye/main i386 libistack-commons-java all 3.0.6-5 [145 kB] Get: 190 http://deb.debian.org/debian bullseye/main i386 libcodemodel-java all 2.6+jaxb2.3.0.1-10 [163 kB] Get: 191 http://deb.debian.org/debian bullseye/main i386 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 192 http://deb.debian.org/debian bullseye/main i386 libcommons-pool-java all 1.6-4 [109 kB] Get: 193 http://deb.debian.org/debian bullseye/main i386 libcommons-dbcp-java all 1.4-7 [157 kB] Get: 194 http://deb.debian.org/debian bullseye/main i386 libcommons-math-java all 2.2-7 [928 kB] Get: 195 http://deb.debian.org/debian bullseye/main i386 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 196 http://deb.debian.org/debian bullseye/main i386 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 197 http://deb.debian.org/debian bullseye/main i386 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 198 http://deb.debian.org/debian bullseye/main i386 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 199 http://deb.debian.org/debian bullseye/main i386 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 200 http://deb.debian.org/debian bullseye/main i386 libxsom-java all 2.3.0.1-10 [396 kB] Get: 201 http://deb.debian.org/debian bullseye/main i386 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 202 http://deb.debian.org/debian bullseye/main i386 libgoogle-gson-java all 2.8.6-1 [225 kB] Get: 203 http://deb.debian.org/debian bullseye/main i386 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 204 http://deb.debian.org/debian bullseye/main i386 libhsqldb-java all 2.5.1-1 [1556 kB] Get: 205 http://deb.debian.org/debian bullseye/main i386 libitext5-java all 5.5.13.2-1 [2630 kB] Get: 206 http://deb.debian.org/debian bullseye/main i386 librngom-java all 2.3.0.1-10 [288 kB] Get: 207 http://deb.debian.org/debian bullseye/main i386 libtxw2-java all 2.3.0.1-10 [134 kB] Get: 208 http://deb.debian.org/debian bullseye/main i386 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 209 http://deb.debian.org/debian bullseye/main i386 libjaxb-java all 2.3.0.1-10 [1954 kB] Get: 210 http://deb.debian.org/debian bullseye/main i386 libjgraph-java all 5.12.4.2+dfsg-5.1 [205 kB] Get: 211 http://deb.debian.org/debian bullseye/main i386 libjgrapht0.8-java all 0.8.3-5 [214 kB] Get: 212 http://deb.debian.org/debian bullseye/main i386 libnaga-java all 3.0+svn80-4 [42.9 kB] Get: 213 http://deb.debian.org/debian bullseye/main i386 libjmol-java all 14.6.4+2016.11.05+dfsg1-4 [6393 kB] Get: 214 http://deb.debian.org/debian bullseye/main i386 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 215 http://deb.debian.org/debian bullseye/main i386 liblightcouch-java all 0.0.6-1.1 [65.2 kB] Get: 216 http://deb.debian.org/debian bullseye/main i386 libmongodb-java all 3.6.3-2 [1901 kB] Get: 217 http://deb.debian.org/debian bullseye/main i386 liblog4j2-java all 2.13.3-1 [1979 kB] Get: 218 http://deb.debian.org/debian bullseye/main i386 libnetx-java all 0.5-4 [138 kB] Get: 219 http://deb.debian.org/debian bullseye/main i386 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 220 http://deb.debian.org/debian bullseye/main i386 libxmlunit-java all 1.6-2 [100 kB] Get: 221 http://deb.debian.org/debian bullseye/main i386 rdfind i386 1.4.1-1+b2 [43.2 kB] Fetched 421 MB in 1min 10s (6017 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_i386.deb ... 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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 ... 20542 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:i386. 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(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 ... 20963 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_i386.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_6.3_all.deb ... Unpacking netbase (6.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... 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Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libnspr4:i386. Preparing to unpack .../010-libnspr4_2%3a4.29-1_i386.deb ... Unpacking libnspr4:i386 (2:4.29-1) ... Selecting previously unselected package libnss3:i386. Preparing to unpack .../011-libnss3_2%3a3.61-1_i386.deb ... Unpacking libnss3:i386 (2:3.61-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../012-ca-certificates-java_20190909_all.deb ... Unpacking ca-certificates-java (20190909) ... Selecting previously unselected package java-common. Preparing to unpack .../013-java-common_0.72_all.deb ... Unpacking java-common (0.72) ... Selecting previously unselected package libavahi-common-data:i386. Preparing to unpack .../014-libavahi-common-data_0.8-5_i386.deb ... Unpacking libavahi-common-data:i386 (0.8-5) ... Selecting previously unselected package libavahi-common3:i386. Preparing to unpack .../015-libavahi-common3_0.8-5_i386.deb ... Unpacking libavahi-common3:i386 (0.8-5) ... Selecting previously unselected package libdbus-1-3:i386. Preparing to unpack .../016-libdbus-1-3_1.12.20-2_i386.deb ... Unpacking libdbus-1-3:i386 (1.12.20-2) ... Selecting previously unselected package libavahi-client3:i386. Preparing to unpack .../017-libavahi-client3_0.8-5_i386.deb ... Unpacking libavahi-client3:i386 (0.8-5) ... Selecting previously unselected package libcups2:i386. Preparing to unpack .../018-libcups2_2.3.3op2-3+deb11u1_i386.deb ... Unpacking libcups2:i386 (2.3.3op2-3+deb11u1) ... Selecting previously unselected package liblcms2-2:i386. Preparing to unpack .../019-liblcms2-2_2.12~rc1-2_i386.deb ... Unpacking liblcms2-2:i386 (2.12~rc1-2) ... Selecting previously unselected package libjpeg62-turbo:i386. Preparing to unpack .../020-libjpeg62-turbo_1%3a2.0.6-4_i386.deb ... Unpacking libjpeg62-turbo:i386 (1:2.0.6-4) ... Selecting previously unselected package libbrotli1:i386. 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Selecting previously unselected package libasound2-data. Preparing to unpack .../027-libasound2-data_1.2.4-1.1_all.deb ... Unpacking libasound2-data (1.2.4-1.1) ... Selecting previously unselected package libasound2:i386. Preparing to unpack .../028-libasound2_1.2.4-1.1_i386.deb ... Unpacking libasound2:i386 (1.2.4-1.1) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../029-libglib2.0-0_2.66.8-1_i386.deb ... Unpacking libglib2.0-0:i386 (2.66.8-1) ... Selecting previously unselected package libgraphite2-3:i386. Preparing to unpack .../030-libgraphite2-3_1.3.14-1_i386.deb ... Unpacking libgraphite2-3:i386 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:i386. Preparing to unpack .../031-libharfbuzz0b_2.7.4-1_i386.deb ... Unpacking libharfbuzz0b:i386 (2.7.4-1) ... Selecting previously unselected package libpcsclite1:i386. Preparing to unpack .../032-libpcsclite1_1.9.1-1_i386.deb ... Unpacking libpcsclite1:i386 (1.9.1-1) ... Selecting previously unselected package openjdk-11-jre-headless:i386. Preparing to unpack .../033-openjdk-11-jre-headless_11.0.11+9-1_i386.deb ... Unpacking openjdk-11-jre-headless:i386 (11.0.11+9-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../034-default-jre-headless_2%3a1.11-72_i386.deb ... Unpacking default-jre-headless (2:1.11-72) ... Selecting previously unselected package ant. Preparing to unpack .../035-ant_1.10.9-4_all.deb ... Unpacking ant (1.10.9-4) ... Selecting previously unselected package ant-contrib. Preparing to unpack .../036-ant-contrib_1.0~b3+svn177-12_all.deb ... Unpacking ant-contrib (1.0~b3+svn177-12) ... Selecting previously unselected package ant-optional. Preparing to unpack .../037-ant-optional_1.10.9-4_all.deb ... Unpacking ant-optional (1.10.9-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../038-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... 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Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../046-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../047-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../048-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../049-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../050-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxmlunit-java (1.6-2) ... Setting up patchutils (0.4.2-1) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libmaven-resolver-java (1.4.2-3) ... Setting up libfreetype6:i386 (2.10.4+dfsg-1) ... Setting up libguava-java (29.0-6) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up ucf (3.0043) ... Setting up libcommons-lang3-java (3.11-1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up librngom-java (2.3.0.1-10) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up gpgconf (2.2.27-2) ... Setting up libharfbuzz0b:i386 (2.7.4-1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libxsom-java (2.3.0.1-10) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libavahi-client3:i386 (0.8-5) ... Setting up libio-socket-ssl-perl (2.069-1) ... Setting up gpg (2.2.27-2) ... Setting up libjmol-java (14.6.4+2016.11.05+dfsg1-4) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up gnupg-utils (2.2.27-2) ... Setting up libhttp-message-perl (6.28-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhttp-negotiate-perl (6.01-1) ... Setting up gpg-agent (2.2.27-2) ... Setting up libcommons-compress-java (1.20-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libcommons-io-java (2.8.0-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up gpgsm (2.2.27-2) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libguice-java (4.2.3-2) ... Setting up dh-autoreconf (20) ... Setting up dirmngr (2.2.27-2) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up gpg-wks-server (2.2.27-2) ... Setting up libcups2:i386 (2.3.3op2-3+deb11u1) ... Setting up libhttpclient-java (4.5.13-2) ... Setting up liblightcouch-java (0.0.6-1.1) ... Setting up libwagon-http-java (3.3.4-1) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfontconfig1:i386 (2.13.1-4.2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up python3.9 (3.9.2-1) ... Setting up libplexus-io-java (3.2.0-1.1) ... Setting up gpg-wks-client (2.2.27-2) ... Setting up libmaven3-core-java (3.6.3-5) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.004004-1) ... Setting up liblog4j2-java (2.13.3-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up gnupg (2.2.27-2) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up libwww-perl (6.52-1) ... Setting up openjdk-11-jre-headless:i386 (11.0.11+9-1) ... 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/jjs to provide /usr/bin/jjs (jjs) 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/rmid to provide /usr/bin/rmid (rmid) 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/pack200 to provide /usr/bin/pack200 (pack200) 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/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 (11.0.11+9-1) ... 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/jfr to provide /usr/bin/jfr (jfr) 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 default-jdk-headless (2:1.11-72) ... Setting up devscripts (2.21.2) ... Setting up ant (1.10.9-4) ... Setting up javahelper (0.78) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:Izenpe.com.pem Adding debian:GTS_Root_R4.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Certigna.pem Adding debian:ACCVRAIZ1.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:ISRG_Root_X1.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:GTS_Root_R3.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:GTS_Root_R2.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:DST_Root_CA_X3.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:SecureTrust_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:EC-ACC.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:GTS_Root_R1.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem done. Setting up junit4 (4.13.1-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up ant-contrib (1.0~b3+svn177-12) ... Setting up ant-optional (1.10.9-4) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10) ... Setting up libtxw2-java (2.3.0.1-10) ... Setting up libjaxb-java (2.3.0.1-10) ... Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... 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 (1.25.3-1.1). 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-3.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Paul Gevers dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dpkg: warning: --compare-versions used with obsolete relation operator '>' dh clean --with javahelper jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' 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 find . -type f -name \*.java.json-simple \ -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' debian/rules build dpkg: warning: --compare-versions used with obsolete relation operator '>' 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' dpkg: warning: --compare-versions used with obsolete relation operator '>' 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' dpkg: warning: --compare-versions used with obsolete relation operator '>' find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ -e 's,@JSON_SIMPLE_PACKAGE@,org.json.simple,' \ {} \; -print ./biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java 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: 14 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 359 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-forester/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL Total time: 55 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: 28 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: 16 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 45 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 1 file to /build/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL Total time: 21 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 32 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/xml/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/convertor/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/package-info.class [copy] Copying 11 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL Total time: 20 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 30 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 1 file to /build/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL Total time: 8 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 19 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes/org/biojava/nbio/sequencing/io/fastq/package-info.class [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL Total time: 10 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 483 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: /build/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 64 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL Total time: 35 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: 22 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: 6 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 34 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 2 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL Total time: 6 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 13 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/ronn/package-info.class [javac] Creating empty /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/data/sequence/package-info.class [copy] Copying 11 files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL Total time: 10 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 1 source file to /build/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [copy] Warning: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL Total time: 4 seconds cd biojava-ws && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 20 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [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: 13 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 46 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [copy] Copying 1 file to /build/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes jar: [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL Total time: 28 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] Debian build on Java 9+ detected: Adding the -Xdoclint:none option [javadoc] Javadoc execution [javadoc] Loading source files for package org.biojava.nbio.aaproperties... 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[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: 1 minute 38 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' dpkg: warning: --compare-versions used with obsolete relation operator '>' 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: 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-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 11.0.11 [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: 0.405 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.405 sec [junit] [junit] Testcase: testGetIndexOf took 0.069 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.008 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.002 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetNumGaps took 0.001 sec [junit] Testcase: testGetStart took 0.001 sec [junit] Testcase: testGetSequenceIndexAt took 0.001 sec [junit] Testcase: testGetAccession took 0 sec [junit] Testcase: testToString took 0.021 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0.001 sec [junit] Testcase: testCountCompounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAt took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.018 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.003 sec [junit] Testcase: testGetOriginalSequence took 0.001 sec [junit] Testcase: testGetCompoundAt took 0.001 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testIsCircular took 0.001 sec [junit] Testcase: testGetEnd took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0.001 sec [junit] Testcase: testGetOverlapCount took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetLocationInAlignment took 0.009 sec [junit] Testcase: testIterator took 0.001 sec [junit] Testcase: testGetSequenceAsString took 0.001 sec [junit] Testcase: testGetLastIndexOf took 0.001 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.003 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: 0.665 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.665 sec [junit] [junit] Testcase: testGetIndexOf took 0.055 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequenceInt took 0.002 sec [junit] Testcase: testToStringInt took 0.008 sec [junit] Testcase: testToString took 0.001 sec [junit] Testcase: testToStringFormatted took 0.017 sec [junit] Testcase: testSimpleProfile took 0 sec [junit] Testcase: testGetSize took 0 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec [junit] Testcase: testGetAlignedSequences took 0 sec [junit] Testcase: testGetOriginalSequences took 0.001 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0 sec [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec [junit] Testcase: testGetIndicesAt took 0.093 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.415 sec [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec [junit] Testcase: testGetLength took 0.001 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 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetCompoundsAt took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec [junit] Testcase: testIterator took 0 sec [junit] Testcase: testGetLastIndexOf took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0.001 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.065 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0 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 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetCompoundInQueryAt took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumIdenticals took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInTargetAt took 0 sec [junit] Testcase: testGetIndexInQueryAt took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumSimilars took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0 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: 0.079 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetAlignment took 0.069 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: 0.446 sec [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.446 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] Jun 24, 2021 3:42:39 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Jun 24, 2021 3:42:39 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testConstructorWithEvalueHspFilter took 0.291 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 0.127 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0.005 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: 28 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 11.0.11 [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: 0.13 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.13 sec [junit] [junit] Testcase: testGetQuery took 0.054 sec [junit] Testcase: testGetScore took 0.053 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 sec [junit] [junit] Testcase: testGetQuery took 0.053 sec [junit] Testcase: testGetScore took 0.113 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.002 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetTarget took 0.001 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: 0.249 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.249 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 0.182 sec [junit] Testcase: testToString took 0.003 sec [junit] Testcase: testGetScoreMatrix took 0.004 sec [junit] Testcase: testGetRoot took 0.036 sec [junit] Testcase: testGetSequences took 0.003 sec [junit] Testcase: testGetDistanceMatrix took 0.002 sec [junit] Testcase: testGetAllPairsScores took 0.002 sec [junit] Testcase: testIterator took 0.002 sec [junit] Running org.biojava.nbio.alignment.LocalAlignmentTest [junit] Testsuite: org.biojava.nbio.alignment.LocalAlignmentTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec [junit] [junit] Testcase: shouldAllowZeroLengthMatches took 0.084 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: 0.506 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.506 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.055 sec [junit] Testcase: testGetGapPenalty took 0.001 sec [junit] Testcase: testGetComputationTime took 0.019 sec [junit] Testcase: should_align_middle_anchor took 0.02 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testNeedlemanWunsch took 0 sec [junit] Testcase: should_align_all_anchored took 0 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.001 sec [junit] Testcase: should_align_multiple_anchors took 0.001 sec [junit] Testcase: testAnchoredDNAAlignment took 0.003 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: should_align_ending_anchor took 0 sec [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec [junit] Testcase: testComplex took 0.008 sec [junit] Testcase: testGetScoreMatrixAsString took 0.015 sec [junit] Testcase: should_align_starting_anchor took 0 sec [junit] Testcase: anchors_should_not_change_score took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0 sec [junit] Testcase: testIntOverflowBug took 0.361 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: 0.097 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 sec [junit] [junit] Testcase: testOpenPenalty took 0.041 sec [junit] Testcase: testType took 0 sec [junit] Testcase: testExtensionPenalty took 0.001 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec [junit] Testcase: testSimpleGapPenalty took 0.001 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 sec [junit] [junit] Testcase: testGetQuery took 0.081 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testSimpleProfilePair took 0.004 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: 0.194 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.104 sec [junit] Testcase: testGetGapPenalty took 0.003 sec [junit] Testcase: testGetComputationTime took 0.002 sec [junit] Testcase: testGetQuery took 0.002 sec [junit] Testcase: testGetScore took 0.002 sec [junit] Testcase: testGetScoreMatrix took 0.003 sec [junit] Testcase: testGetPair took 0.006 sec [junit] Testcase: testGetProfile took 0.003 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec [junit] Testcase: testGetScoreMatrixAsString took 0.025 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.002 sec [junit] Testcase: testSimpleProfileProfileAligner took 0.002 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.142 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.142 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.081 sec [junit] Testcase: testSetDescription took 0.461 sec [junit] Testcase: testToString took 1.413 sec [junit] Testcase: testCaseEquivalence took 0.001 sec [junit] Testcase: test took 0.026 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.054 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.003 sec [junit] Testcase: testSetName took 0.005 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.003 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: 0.305 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.069 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.11 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.012 sec [junit] Testcase: testGetScoreMatrix took 0.002 sec [junit] Testcase: testGetPair took 0.014 sec [junit] Testcase: testSmithWaterman took 0.008 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.04 sec [junit] Testcase: testSetStoringScoreMatrix took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec [junit] [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.004 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.003 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 0.001 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 sec [junit] [junit] Testcase: testGetComputationTime took 0.136 sec [junit] Testcase: testGuanUberbacher took 0 sec [junit] Testcase: testGetScore took 0 sec [junit] Testcase: testGetPair took 0.004 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: should_align_shorter_target took 0.028 sec [junit] Testcase: should_align_multiple_cuts took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Testcase: should_align_shorter_query took 0 sec BUILD SUCCESSFUL Total time: 24 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 11.0.11 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.069 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.069 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 0.955 sec [junit] Testcase: testExample1 took 0.03 sec [junit] Testcase: testExample2 took 0.005 sec [junit] Testcase: testExample3 took 0.018 sec [junit] Testcase: testExample1WithCSV took 0.036 sec [junit] Testcase: testWithCases took 0.008 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.491 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.491 sec [junit] [junit] Testcase: shortExample1 took 0.038 sec [junit] Testcase: shortExample2 took 1.367 sec [junit] Testcase: shortExample3 took 0.049 sec [junit] Testcase: shortExample4 took 0.009 sec [junit] Testcase: shortExample5 took 0.005 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.712 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.712 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 2.237 sec [junit] Testcase: testExample1 took 0.194 sec [junit] Testcase: testExample2 took 0.016 sec [junit] Testcase: testExample3 took 0.022 sec [junit] Testcase: testExample1WithCSV took 0.178 sec [junit] Testcase: testWithCases took 0.019 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.156 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.156 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 0.058 sec [junit] Testcase: testMolecularWeightXMLSingleFile took 1.288 sec [junit] Testcase: testEnrichment took 1.176 sec [junit] Testcase: testApliphaticIndex took 0.003 sec [junit] Testcase: testMolecularWeightXMLNull took 0.013 sec [junit] Testcase: testApliphaticIndexNull took 0 sec [junit] Testcase: testIsoelectricPointExpasy took 0.932 sec [junit] Testcase: testAbsorbanceNull took 0.001 sec [junit] Testcase: testIsoelectricPointNull took 0 sec [junit] Testcase: testAverageHydropathy took 0.041 sec [junit] Testcase: testExtinctionCoefficient took 0.002 sec [junit] Testcase: testAAComposition took 0.002 sec [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.364 sec [junit] Testcase: testMolecularWeight took 0.001 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.003 sec [junit] Testcase: testNetChargeNull took 0.001 sec [junit] Testcase: testExtinctionCoefficientNull took 0 sec [junit] Testcase: testNetCharge took 0.123 sec [junit] Testcase: testEnrichmentNull took 0.001 sec [junit] Testcase: testInstabilityIndexNull took 0 sec [junit] Testcase: testAverageHydropathyNull took 0 sec [junit] Testcase: testMolecularWeightXML took 0.067 sec [junit] Testcase: testInstabilityIndex took 0.001 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] [junit] Testcase: testFake took 0.002 sec [junit] Running org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 sec [junit] [junit] Testcase: testFakeTest took 0.106 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.786 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.786 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 0.412 sec [junit] Testcase: readWithIDXml took 0.195 sec [junit] Testcase: readMinXml took 0.046 sec [junit] Testcase: readAdvancedXml took 0.042 sec [junit] Testcase: generateXml took 0.029 sec [junit] Testcase: readXml took 0.048 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.628 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.628 sec [junit] [junit] Testcase: generateSchema took 0.414 sec [junit] Testcase: generateXml took 0.054 sec [junit] Testcase: readXml took 0.143 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: 0.024 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec [junit] [junit] Testcase: testFake took 0.015 sec BUILD SUCCESSFUL Total time: 27 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 11.0.11 BUILD SUCCESSFUL Total time: 2 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 14 source files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 74 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 19 files to /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes test: [echo] Using java version 11.0.11 [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: 1.273 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.273 sec [junit] [junit] Testcase: testConvert took 1.259 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: 0.023 sec [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec [junit] [junit] Testcase: testBuildAppendSequence took 0.004 sec [junit] Testcase: testBuildNullDescription took 0 sec [junit] Testcase: testBuildAppendQuality took 0 sec [junit] Testcase: testBuild took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0 sec [junit] Testcase: testBuildNullSequence took 0 sec [junit] Testcase: testBuildMissingDescription took 0 sec [junit] Testcase: testBuildNullVariant took 0 sec [junit] Testcase: testBuildDefault took 0 sec [junit] Testcase: testBuildMissingSequence took 0 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: 0.054 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec [junit] [junit] Testcase: testImmutable took 0.003 sec [junit] Testcase: testBuilder took 0.003 sec [junit] Testcase: testVariant took 0.001 sec [junit] Testcase: testQuality took 0.031 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: 0.203 sec [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec [junit] [junit] Testcase: testErrorProbabilitiesNullFastq took 0.002 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0 sec [junit] Testcase: testConvertNullVariant took 0.001 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.131 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0.001 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 0.001 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0.001 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.003 sec [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0 sec [junit] Testcase: testQualityScores took 0.005 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec [junit] Testcase: testCreateDNASequence took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec [junit] Testcase: testQualityScoresIntArray took 0.001 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testToList took 0 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: 0.018 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] [junit] Testcase: testParseFastqVariant took 0.003 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: 0.183 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec [junit] [junit] Testcase: testFullRangeAsIllumina took 0.044 sec [junit] Testcase: testWrappingAsIllumina took 0.002 sec [junit] Testcase: testValidateDescription took 0.007 sec [junit] Testcase: testValidateRepeatDescription took 0.003 sec [junit] Testcase: testMiscDnaAsIllumina took 0.002 sec [junit] Testcase: testMiscRnaAsIllumina took 0.002 sec [junit] Testcase: testLongReadsAsIllumina took 0.004 sec [junit] Testcase: testParseNullReadable took 0 sec [junit] Testcase: testReadRoundTripSingleFile took 0.048 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.022 sec [junit] Testcase: testParse took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0.001 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0 sec [junit] Testcase: testWrappedQuality took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.007 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.003 sec [junit] Testcase: testWriteFileIterable took 0.016 sec [junit] Testcase: testWriteOutputStreamIterable took 0 sec [junit] Testcase: testAppendIterable took 0.001 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: 0.253 sec [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.253 sec [junit] [junit] Testcase: testMiscRnaAsSanger took 0.053 sec [junit] Testcase: testFullRangeAsSanger took 0.006 sec [junit] Testcase: testWrappingOriginal took 0.004 sec [junit] Testcase: testLongReadsOriginal took 0.008 sec [junit] Testcase: testMiscDnaOriginal took 0.003 sec [junit] Testcase: testMiscRnaOriginal took 0.002 sec [junit] Testcase: testValidateDescription took 0.009 sec [junit] Testcase: testValidateRepeatDescription took 0.002 sec [junit] Testcase: testFullRangeOriginal took 0.001 sec [junit] Testcase: testWrappingAsSanger took 0.002 sec [junit] Testcase: testLongReadsAsSanger took 0.003 sec [junit] Testcase: testMiscDnaAsSanger took 0.001 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.016 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.018 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 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 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 sec [junit] [junit] Testcase: testConvertNotSangerVariant took 0.005 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.003 sec [junit] Testcase: testWriteFileIterable took 0.039 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 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 sec [junit] [junit] Testcase: testMiscRnaAsSolexa took 0.035 sec [junit] Testcase: testFullRangeAsSolexa took 0.003 sec [junit] Testcase: testValidateDescription took 0.007 sec [junit] Testcase: testValidateRepeatDescription took 0.003 sec [junit] Testcase: testWrappingAsSolexa took 0.002 sec [junit] Testcase: testLongReadsAsSolexa took 0.003 sec [junit] Testcase: testMiscDnaAsSolexa took 0.001 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.017 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.019 sec [junit] Testcase: testParse took 0 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 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: 0.04 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] [junit] Testcase: testConvertNotSolexaVariant took 0.006 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.003 sec [junit] Testcase: testWriteFileIterable took 0.016 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.StreamingFastqParserTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] [junit] Testcase: testStreamNullVariant took 0.002 sec [junit] Testcase: testStreamNullListener took 0.002 sec [junit] Testcase: testStreamNullReadable took 0 sec BUILD SUCCESSFUL Total time: 17 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 11.0.11 [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: 0.01 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] [junit] Testcase: testMe took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 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: 0.093 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec [junit] [junit] Testcase: testGetColor took 0.051 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec [junit] Testcase: testGetSelection took 0.004 sec [junit] Testcase: testRepaint took 0 sec [junit] Testcase: testSetSelection took 0.001 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec [junit] Testcase: testSetStyle took 0 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL Total time: 9 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 11.0.11 BUILD SUCCESSFUL Total time: 3 seconds make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dpkg: warning: --compare-versions used with obsolete relation operator '>' 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' dpkg: warning: --compare-versions used with obsolete relation operator '>' jh_installjavadoc rdfind -makesymlinks true -followsymlinks true \ $(dpkg -L $(apt-cache show default-jdk-doc | grep Depends | awk '{print $2}') | grep /usr/share/doc/ | head -n1) \ debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java/ Now scanning "/usr/share/doc/openjdk-11-doc", found 10339 files. Now scanning "debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java", found 1873 files. Now have 12212 files in total. Removed 1 files due to nonunique device and inode. Total size is 322289148 bytes or 307 MiB Removed 7227 files due to unique sizes from list.4984 files left. Now eliminating candidates based on first bytes:removed 788 files from list.4196 files left. Now eliminating candidates based on last bytes:removed 19 files from list.4177 files left. Now eliminating candidates based on sha1 checksum:removed 4139 files from list.38 files left. It seems like you have 38 files that are not unique Totally, 1 MiB can be reduced. Now making results file results.txt Now making symbolic links. creating Failed moving /usr/share/doc/openjdk-11-doc/api/jquery/external/jquery/jquery.js to a temporary file Failed to make symlink /usr/share/doc/openjdk-11-doc/api/jquery/external/jquery/jquery.js to /usr/share/doc/openjdk-11-doc/api/jquery/jquery-3.5.1.js Making 19 links. make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-3.1_all.deb'. dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb'. dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava4-live_4.2.12+dfsg-3.1_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/30254 and its subdirectories I: Current time: Thu Jun 24 03:45:27 -12 2021 I: pbuilder-time-stamp: 1624549527 Thu Jun 24 15:45:28 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Thu Jun 24 15:45:28 UTC 2021 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Thu Jun 24 15:48:19 UTC 2021 I: Deleting $TMPDIR on ionos6-i386.debian.net. Thu Jun 24 15:48:20 UTC 2021 I: biojava4-live_4.2.12+dfsg-3.1_i386.changes: Format: 1.8 Date: Mon, 13 Jul 2020 21:28:31 +0200 Source: biojava4-live Binary: libbiojava4-java libbiojava4-java-doc libbiojava4.0-java Architecture: all Version: 4.2.12+dfsg-3.1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Paul Gevers 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) Closes: 964982 Changes: biojava4-live (4.2.12+dfsg-3.1) unstable; urgency=medium . * Non-maintainer upload. * source only upload to enable migration (Closes: #964982) Checksums-Sha1: b8c5f71fd380fee61e98924e290291a80796aa11 11806 biojava4-live_4.2.12+dfsg-3.1_i386.buildinfo ae0a5ee6af3833ac22063f0f554bcc731c89beda 1978896 libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb 5b319d321b8eca66a4d9afc0827001e40debb3f7 4744 libbiojava4-java_4.2.12+dfsg-3.1_all.deb 5cf7eb9b5f2a48343e8bef4055dc643f69233da4 5451904 libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb Checksums-Sha256: 440c74ecb663b6cee263a695c40a475fbb1631a44daaf8180f7644cf8beb91f4 11806 biojava4-live_4.2.12+dfsg-3.1_i386.buildinfo 3f371439d1381ef5979aa1e01e96c19af9e9c5898a74abea51201a41ec77c273 1978896 libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb 54191b6ed2733616868ef8e04a93024c329cf06dcf34b9d645c0d1aaddf53496 4744 libbiojava4-java_4.2.12+dfsg-3.1_all.deb 9dcec957ab84530e7548232d8904478982d8193bf4a53d27c4be2e00a9fccbc3 5451904 libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb Files: 80487c266fd40b02bddf9ff8f3bc3f1e 11806 java optional biojava4-live_4.2.12+dfsg-3.1_i386.buildinfo e3c48567995921d1cb83fddccccd38cf 1978896 doc optional libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb 815133db2aba2c2b38cfc429a98a3227 4744 java optional libbiojava4-java_4.2.12+dfsg-3.1_all.deb d2f1883913b572e64f504ca7d5554d8b 5451904 java optional libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb Thu Jun 24 15:48:21 UTC 2021 I: diffoscope 172 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.6lQib42wHB/biojava4-live_4.2.12+dfsg-3.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.6lQib42wHB/biojava4-live_4.2.12+dfsg-3.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.6lQib42wHB/biojava4-live_4.2.12+dfsg-3.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.6lQib42wHB/b1/biojava4-live_4.2.12+dfsg-3.1_i386.changes /srv/reproducible-results/rbuild-debian/tmp.6lQib42wHB/b2/biojava4-live_4.2.12+dfsg-3.1_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: 0.321s) 0.321s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.093s) 0.093s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Jun 24 15:48:22 UTC 2021 I: diffoscope 172 found no differences in the changes files, and a .buildinfo file also exists. Thu Jun 24 15:48:22 UTC 2021 I: biojava4-live from bullseye built successfully and reproducibly on i386. Thu Jun 24 15:48:24 UTC 2021 I: Submitting .buildinfo files to external archives: Thu Jun 24 15:48:24 UTC 2021 I: Submitting 16K b1/biojava4-live_4.2.12+dfsg-3.1_i386.buildinfo.asc Thu Jun 24 15:48:25 UTC 2021 I: Submitting 16K b2/biojava4-live_4.2.12+dfsg-3.1_i386.buildinfo.asc Thu Jun 24 15:48:26 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jun 24 15:48:26 UTC 2021 I: Done submitting .buildinfo files. Thu Jun 24 15:48:26 UTC 2021 I: Removing signed biojava4-live_4.2.12+dfsg-3.1_i386.buildinfo.asc files: removed './b1/biojava4-live_4.2.12+dfsg-3.1_i386.buildinfo.asc' removed './b2/biojava4-live_4.2.12+dfsg-3.1_i386.buildinfo.asc'