Fri Aug 13 22:37:47 UTC 2021 I: starting to build biojava4-live/bullseye/armhf on jenkins on '2021-08-13 22:37' Fri Aug 13 22:37:48 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_45/3057/console.log Fri Aug 13 22:37:48 UTC 2021 I: Downloading source for bullseye/biojava4-live=4.2.12+dfsg-3.1 --2021-08-13 22:37:48-- 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% 272M=0s 2021-08-13 22:37:48 (272 MB/s) - ‘biojava4-live_4.2.12+dfsg-3.1.dsc’ saved [2489/2489] Fri Aug 13 22:37:48 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----- Fri Aug 13 22:37:48 UTC 2021 I: Checking whether the package is not for us Fri Aug 13 22:37:48 UTC 2021 I: Starting 1st build on remote node jtx1c-armhf-rb.debian.net. Fri Aug 13 22:37:48 UTC 2021 I: Preparing to do remote build '1' on jtx1c-armhf-rb.debian.net. Fri Aug 13 22:49:00 UTC 2021 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 13 10:37:54 -12 2021 I: pbuilder-time-stamp: 1628894274 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: 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.Q6S4UCw1/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/21715/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='1cb17b4eb806462e9d5c8e812767557b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='21715' 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.I27oqKZ04L/pbuilderrc_eBGw --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-3.1.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux jtx1c 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jul 28 07:09 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 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 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 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 88524 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 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 11 21:26 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 28 07:09 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/21715/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), ant, libcommons-dbcp-java, libhsqldb-java, libcommons-collections3-java, libcommons-pool-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libguava-java (>= 17.0), libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java (>= 14.6.4), libvecmath-java, default-jdk-headless, junit4, javahelper, ant-optional, ant-contrib, libhamcrest-java, libjson-simple-java (>= 1.1.1), liblog4j2-java, libslf4j-java, libxmlunit-java, libjgrapht-java, libjaxb-api-java, libjaxb-java, libnetx-java, default-jdk-doc, rdfind dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 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 301 MB of archives. After unpacking 791 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf libpython3.9-minimal armhf 3.9.2-1 [790 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf python3.9-minimal armhf 3.9.2-1 [1630 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libmpdec3 armhf 2.5.1-1 [74.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf libpython3.9-stdlib armhf 3.9.2-1 [1608 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf python3.9 armhf 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf python3 armhf 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf netbase all 6.3 [19.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf openssl armhf 1.1.1k-1 [826 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf ca-certificates all 20210119 [158 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf ucf all 3.0043 [74.0 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libnspr4 armhf 2:4.29-1 [90.7 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libnss3 armhf 2:3.61-1 [1114 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf ca-certificates-java all 20190909 [15.7 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf java-common all 0.72 [14.5 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf libavahi-common-data armhf 0.8-5 [123 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libavahi-common3 armhf 0.8-5 [55.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libdbus-1-3 armhf 1.12.20-2 [196 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libavahi-client3 armhf 0.8-5 [58.5 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libcups2 armhf 2.3.3op2-3+deb11u1 [317 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf liblcms2-2 armhf 2.12~rc1-2 [123 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [123 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libpng16-16 armhf 1.6.37-3 [277 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [357 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf fonts-dejavu-core all 2.37-2 [1069 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf fontconfig-config all 2.13.1-4.2 [281 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libfontconfig1 armhf 2.13.1-4.2 [329 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libasound2 armhf 1.2.4-1.1 [310 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libgraphite2-3 armhf 1.3.14-1 [70.5 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf libharfbuzz0b armhf 2.7.4-1 [1427 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libpcsclite1 armhf 1.9.1-1 [57.2 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf openjdk-11-jre-headless armhf 11.0.12+7-2 [32.9 MB] Get: 51 http://deb.debian.org/debian bullseye/main armhf default-jre-headless armhf 2:1.11-72 [10.9 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf ant all 1.10.9-4 [2118 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf ant-optional all 1.10.9-4 [381 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf dctrl-tools armhf 2.24-3 [96.0 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 64 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 65 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 66 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 67 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 69 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 70 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 72 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 73 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf openjdk-11-doc all 11.0.12+7-2 [13.5 MB] Get: 78 http://deb.debian.org/debian bullseye/main armhf default-jdk-doc armhf 2:1.11-72 [11.0 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf openjdk-11-jdk-headless armhf 11.0.12+7-2 [174 MB] Get: 80 http://deb.debian.org/debian bullseye/main armhf default-jdk-headless armhf 2:1.11-72 [1100 B] Get: 81 http://deb.debian.org/debian bullseye/main armhf libassuan0 armhf 2.5.3-7.1 [44.2 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf gpgconf armhf 2.2.27-2 [532 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf libksba8 armhf 1.5.0-3 [105 kB] Get: 84 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 85 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf libnpth0 armhf 1.6-3 [17.8 kB] Get: 88 http://deb.debian.org/debian bullseye/main armhf dirmngr armhf 2.2.27-2 [722 kB] Get: 89 http://deb.debian.org/debian bullseye/main armhf gnupg-l10n all 2.2.27-2 [1084 kB] Get: 90 http://deb.debian.org/debian bullseye/main armhf gnupg-utils armhf 2.2.27-2 [835 kB] Get: 91 http://deb.debian.org/debian bullseye/main armhf gpg armhf 2.2.27-2 [868 kB] Get: 92 http://deb.debian.org/debian bullseye/main armhf pinentry-curses armhf 1.1.0-4 [60.6 kB] Get: 93 http://deb.debian.org/debian bullseye/main armhf gpg-agent armhf 2.2.27-2 [630 kB] Get: 94 http://deb.debian.org/debian bullseye/main armhf gpg-wks-client armhf 2.2.27-2 [509 kB] Get: 95 http://deb.debian.org/debian bullseye/main armhf gpg-wks-server armhf 2.2.27-2 [503 kB] Get: 96 http://deb.debian.org/debian bullseye/main armhf gpgsm armhf 2.2.27-2 [618 kB] Get: 97 http://deb.debian.org/debian bullseye/main armhf gnupg all 2.2.27-2 [825 kB] Get: 98 http://deb.debian.org/debian bullseye/main armhf libfile-dirlist-perl all 0.05-2 [7444 B] Get: 99 http://deb.debian.org/debian bullseye/main armhf libfile-which-perl all 1.23-1 [16.6 kB] Get: 100 http://deb.debian.org/debian bullseye/main armhf libfile-homedir-perl all 1.006-1 [43.8 kB] Get: 101 http://deb.debian.org/debian bullseye/main armhf libfile-touch-perl all 0.11-1 [9254 B] Get: 102 http://deb.debian.org/debian bullseye/main armhf libio-pty-perl armhf 1:1.15-2 [36.2 kB] Get: 103 http://deb.debian.org/debian bullseye/main armhf libipc-run-perl all 20200505.0-1 [102 kB] Get: 104 http://deb.debian.org/debian bullseye/main armhf libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get: 105 http://deb.debian.org/debian bullseye/main armhf libb-hooks-op-check-perl armhf 0.22-1+b3 [11.0 kB] Get: 106 http://deb.debian.org/debian bullseye/main armhf libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 107 http://deb.debian.org/debian bullseye/main armhf libdevel-callchecker-perl armhf 0.008-1+b2 [15.7 kB] Get: 108 http://deb.debian.org/debian bullseye/main armhf libparams-classify-perl armhf 0.015-1+b3 [24.5 kB] Get: 109 http://deb.debian.org/debian bullseye/main armhf libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 110 http://deb.debian.org/debian bullseye/main armhf libimport-into-perl all 1.002005-1 [11.6 kB] Get: 111 http://deb.debian.org/debian bullseye/main armhf librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 112 http://deb.debian.org/debian bullseye/main armhf libstrictures-perl all 2.000006-1 [18.6 kB] Get: 113 http://deb.debian.org/debian bullseye/main armhf libsub-quote-perl all 2.006006-1 [21.0 kB] Get: 114 http://deb.debian.org/debian bullseye/main armhf libmoo-perl all 2.004004-1 [59.9 kB] Get: 115 http://deb.debian.org/debian bullseye/main armhf libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 116 http://deb.debian.org/debian bullseye/main armhf libtimedate-perl all 2.3300-2 [39.3 kB] Get: 117 http://deb.debian.org/debian bullseye/main armhf libhttp-date-perl all 6.05-1 [10.4 kB] Get: 118 http://deb.debian.org/debian bullseye/main armhf libfile-listing-perl all 6.14-1 [12.4 kB] Get: 119 http://deb.debian.org/debian bullseye/main armhf libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 120 http://deb.debian.org/debian bullseye/main armhf liburi-perl all 5.08-1 [90.6 kB] Get: 121 http://deb.debian.org/debian bullseye/main armhf libhtml-parser-perl armhf 3.75-1+b1 [102 kB] Get: 122 http://deb.debian.org/debian bullseye/main armhf libhtml-tree-perl all 5.07-2 [213 kB] Get: 123 http://deb.debian.org/debian bullseye/main armhf libio-html-perl all 1.004-2 [16.1 kB] Get: 124 http://deb.debian.org/debian bullseye/main armhf liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 125 http://deb.debian.org/debian bullseye/main armhf libhttp-message-perl all 6.28-1 [79.6 kB] Get: 126 http://deb.debian.org/debian bullseye/main armhf libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 127 http://deb.debian.org/debian bullseye/main armhf libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 128 http://deb.debian.org/debian bullseye/main armhf perl-openssl-defaults armhf 5 [7360 B] Get: 129 http://deb.debian.org/debian bullseye/main armhf libnet-ssleay-perl armhf 1.88-3+b1 [303 kB] Get: 130 http://deb.debian.org/debian bullseye/main armhf libio-socket-ssl-perl all 2.069-1 [215 kB] Get: 131 http://deb.debian.org/debian bullseye/main armhf libnet-http-perl all 6.20-1 [25.1 kB] Get: 132 http://deb.debian.org/debian bullseye/main armhf liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 133 http://deb.debian.org/debian bullseye/main armhf libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 134 http://deb.debian.org/debian bullseye/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 135 http://deb.debian.org/debian bullseye/main armhf libwww-perl all 6.52-1 [192 kB] Get: 136 http://deb.debian.org/debian bullseye/main armhf patchutils armhf 0.4.2-1 [72.5 kB] Get: 137 http://deb.debian.org/debian bullseye/main armhf wdiff armhf 1.2.2-2+b1 [121 kB] Get: 138 http://deb.debian.org/debian bullseye/main armhf devscripts armhf 2.21.3 [1092 kB] Get: 139 http://deb.debian.org/debian bullseye/main armhf javahelper all 0.78 [97.2 kB] Get: 140 http://deb.debian.org/debian bullseye/main armhf junit all 3.8.2-9 [110 kB] Get: 141 http://deb.debian.org/debian bullseye/main armhf libhamcrest-java all 1.3-9 [388 kB] Get: 142 http://deb.debian.org/debian bullseye/main armhf junit4 all 4.13.1-2 [347 kB] Get: 143 http://deb.debian.org/debian bullseye/main armhf libactivation-java all 1.2.0-2 [84.7 kB] Get: 144 http://deb.debian.org/debian bullseye/main armhf libaopalliance-java all 20070526-6 [9048 B] Get: 145 http://deb.debian.org/debian bullseye/main armhf libapache-pom-java all 18-1 [4676 B] Get: 146 http://deb.debian.org/debian bullseye/main armhf libargs4j-java all 2.33-1.1 [137 kB] Get: 147 http://deb.debian.org/debian bullseye/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 148 http://deb.debian.org/debian bullseye/main armhf libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 149 http://deb.debian.org/debian bullseye/main armhf libcdi-api-java all 1.2-3 [54.3 kB] Get: 150 http://deb.debian.org/debian bullseye/main armhf libjaxen-java all 1.1.6-4 [214 kB] Get: 151 http://deb.debian.org/debian bullseye/main armhf libdom4j-java all 2.1.3-1 [310 kB] Get: 152 http://deb.debian.org/debian bullseye/main armhf libcommons-parent-java all 43-1 [10.8 kB] Get: 153 http://deb.debian.org/debian bullseye/main armhf libcommons-io-java all 2.8.0-1 [279 kB] Get: 154 http://deb.debian.org/debian bullseye/main armhf libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 155 http://deb.debian.org/debian bullseye/main armhf libcommons-cli-java all 1.4-2 [57.3 kB] Get: 156 http://deb.debian.org/debian bullseye/main armhf libcommons-lang3-java all 3.11-1 [550 kB] Get: 157 http://deb.debian.org/debian bullseye/main armhf libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 158 http://deb.debian.org/debian bullseye/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 159 http://deb.debian.org/debian bullseye/main armhf libguava-java all 29.0-6 [2419 kB] Get: 160 http://deb.debian.org/debian bullseye/main armhf libguice-java all 4.2.3-2 [1435 kB] Get: 161 http://deb.debian.org/debian bullseye/main armhf libmaven-parent-java all 31-2 [5100 B] Get: 162 http://deb.debian.org/debian bullseye/main armhf libplexus-utils2-java all 3.3.0-1 [250 kB] Get: 163 http://deb.debian.org/debian bullseye/main armhf libwagon-provider-api-java all 3.3.4-1 [50.2 kB] Get: 164 http://deb.debian.org/debian bullseye/main armhf libmaven-resolver-java all 1.4.2-3 [556 kB] Get: 165 http://deb.debian.org/debian bullseye/main armhf libplexus-cipher-java all 1.8-2 [15.0 kB] Get: 166 http://deb.debian.org/debian bullseye/main armhf libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 167 http://deb.debian.org/debian bullseye/main armhf libplexus-component-annotations-java all 2.1.0-1 [7620 B] Get: 168 http://deb.debian.org/debian bullseye/main armhf libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 169 http://deb.debian.org/debian bullseye/main armhf libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 170 http://deb.debian.org/debian bullseye/main armhf libslf4j-java all 1.7.30-1 [144 kB] Get: 171 http://deb.debian.org/debian bullseye/main armhf libsisu-inject-java all 0.3.4-2 [347 kB] Get: 172 http://deb.debian.org/debian bullseye/main armhf libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 173 http://deb.debian.org/debian bullseye/main armhf libmaven3-core-java all 3.6.3-5 [1538 kB] Get: 174 http://deb.debian.org/debian bullseye/main armhf libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 175 http://deb.debian.org/debian bullseye/main armhf libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 176 http://deb.debian.org/debian bullseye/main armhf libcommons-compress-java all 1.20-1 [574 kB] Get: 177 http://deb.debian.org/debian bullseye/main armhf libplexus-io-java all 3.2.0-1.1 [65.0 kB] Get: 178 http://deb.debian.org/debian bullseye/main armhf libsnappy1v5 armhf 1.1.8-1 [16.5 kB] Get: 179 http://deb.debian.org/debian bullseye/main armhf libsnappy-jni armhf 1.1.8.3-1 [6800 B] Get: 180 http://deb.debian.org/debian bullseye/main armhf libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 181 http://deb.debian.org/debian bullseye/main armhf libxz-java all 1.8-2 [141 kB] Get: 182 http://deb.debian.org/debian bullseye/main armhf libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 183 http://deb.debian.org/debian bullseye/main armhf libhttpcore-java all 4.4.14-1 [631 kB] Get: 184 http://deb.debian.org/debian bullseye/main armhf libcommons-codec-java all 1.15-1 [292 kB] Get: 185 http://deb.debian.org/debian bullseye/main armhf libcommons-logging-java all 1.2-2 [62.2 kB] Get: 186 http://deb.debian.org/debian bullseye/main armhf libhttpclient-java all 4.5.13-2 [1233 kB] Get: 187 http://deb.debian.org/debian bullseye/main armhf libjsoup-java all 1.10.2-2 [350 kB] Get: 188 http://deb.debian.org/debian bullseye/main armhf libwagon-http-java all 3.3.4-1 [53.9 kB] Get: 189 http://deb.debian.org/debian bullseye/main armhf libistack-commons-java all 3.0.6-5 [145 kB] Get: 190 http://deb.debian.org/debian bullseye/main armhf libcodemodel-java all 2.6+jaxb2.3.0.1-10 [163 kB] Get: 191 http://deb.debian.org/debian bullseye/main armhf libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 192 http://deb.debian.org/debian bullseye/main armhf libcommons-pool-java all 1.6-4 [109 kB] Get: 193 http://deb.debian.org/debian bullseye/main armhf libcommons-dbcp-java all 1.4-7 [157 kB] Get: 194 http://deb.debian.org/debian bullseye/main armhf libcommons-math-java all 2.2-7 [928 kB] Get: 195 http://deb.debian.org/debian bullseye/main armhf libdtd-parser-java all 1.2-1 [64.9 kB] Get: 196 http://deb.debian.org/debian bullseye/main armhf libjaxb-api-java all 2.3.1-1 [119 kB] Get: 197 http://deb.debian.org/debian bullseye/main armhf libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 198 http://deb.debian.org/debian bullseye/main armhf libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 199 http://deb.debian.org/debian bullseye/main armhf librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 200 http://deb.debian.org/debian bullseye/main armhf libxsom-java all 2.3.0.1-10 [396 kB] Get: 201 http://deb.debian.org/debian bullseye/main armhf libfastinfoset-java all 1.2.12-3 [343 kB] Get: 202 http://deb.debian.org/debian bullseye/main armhf libgoogle-gson-java all 2.8.6-1 [225 kB] Get: 203 http://deb.debian.org/debian bullseye/main armhf libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 204 http://deb.debian.org/debian bullseye/main armhf libhsqldb-java all 2.5.1-1 [1556 kB] Get: 205 http://deb.debian.org/debian bullseye/main armhf libitext5-java all 5.5.13.2-1 [2630 kB] Get: 206 http://deb.debian.org/debian bullseye/main armhf librngom-java all 2.3.0.1-10 [288 kB] Get: 207 http://deb.debian.org/debian bullseye/main armhf libtxw2-java all 2.3.0.1-10 [134 kB] Get: 208 http://deb.debian.org/debian bullseye/main armhf libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 209 http://deb.debian.org/debian bullseye/main armhf libjaxb-java all 2.3.0.1-10 [1954 kB] Get: 210 http://deb.debian.org/debian bullseye/main armhf libjgraph-java all 5.12.4.2+dfsg-5.1 [205 kB] Get: 211 http://deb.debian.org/debian bullseye/main armhf libjgrapht0.8-java all 0.8.3-5 [214 kB] Get: 212 http://deb.debian.org/debian bullseye/main armhf libnaga-java all 3.0+svn80-4 [42.9 kB] Get: 213 http://deb.debian.org/debian bullseye/main armhf libjmol-java all 14.6.4+2016.11.05+dfsg1-4 [6393 kB] Get: 214 http://deb.debian.org/debian bullseye/main armhf libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 215 http://deb.debian.org/debian bullseye/main armhf liblightcouch-java all 0.0.6-1.1 [65.2 kB] Get: 216 http://deb.debian.org/debian bullseye/main armhf libmongodb-java all 3.6.3-2 [1901 kB] Get: 217 http://deb.debian.org/debian bullseye/main armhf liblog4j2-java all 2.13.3-1 [1979 kB] Get: 218 http://deb.debian.org/debian bullseye/main armhf libnetx-java all 0.5-4 [138 kB] Get: 219 http://deb.debian.org/debian bullseye/main armhf libvecmath-java all 1.5.2-7 [97.0 kB] Get: 220 http://deb.debian.org/debian bullseye/main armhf libxmlunit-java all 1.6-2 [100 kB] Get: 221 http://deb.debian.org/debian bullseye/main armhf rdfind armhf 1.4.1-1+b2 [37.2 kB] Fetched 301 MB in 42s (7100 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 ... 19398 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../3-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:armhf. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_armhf.deb ... Unpacking libpython3.9-minimal:armhf (3.9.2-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../6-libexpat1_2.2.10-2_armhf.deb ... Unpacking libexpat1:armhf (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_armhf.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:armhf (3.9.2-1) ... Setting up libexpat1:armhf (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20265 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.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:armhf. Preparing to unpack .../2-libmpdec3_2.5.1-1_armhf.deb ... Unpacking libmpdec3:armhf (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../4-libreadline8_8.1-1_armhf.deb ... Unpacking libreadline8:armhf (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:armhf. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_armhf.deb ... Unpacking libpython3.9-stdlib:armhf (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_armhf.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20686 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_armhf.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) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_1.1.1k-1_armhf.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../006-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../009-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libnspr4:armhf. Preparing to unpack .../010-libnspr4_2%3a4.29-1_armhf.deb ... Unpacking libnspr4:armhf (2:4.29-1) ... Selecting previously unselected package libnss3:armhf. Preparing to unpack .../011-libnss3_2%3a3.61-1_armhf.deb ... Unpacking libnss3:armhf (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:armhf. Preparing to unpack .../014-libavahi-common-data_0.8-5_armhf.deb ... Unpacking libavahi-common-data:armhf (0.8-5) ... Selecting previously unselected package libavahi-common3:armhf. Preparing to unpack .../015-libavahi-common3_0.8-5_armhf.deb ... Unpacking libavahi-common3:armhf (0.8-5) ... Selecting previously unselected package libdbus-1-3:armhf. Preparing to unpack .../016-libdbus-1-3_1.12.20-2_armhf.deb ... Unpacking libdbus-1-3:armhf (1.12.20-2) ... Selecting previously unselected package libavahi-client3:armhf. Preparing to unpack .../017-libavahi-client3_0.8-5_armhf.deb ... Unpacking libavahi-client3:armhf (0.8-5) ... Selecting previously unselected package libcups2:armhf. Preparing to unpack .../018-libcups2_2.3.3op2-3+deb11u1_armhf.deb ... Unpacking libcups2:armhf (2.3.3op2-3+deb11u1) ... Selecting previously unselected package liblcms2-2:armhf. Preparing to unpack .../019-liblcms2-2_2.12~rc1-2_armhf.deb ... Unpacking liblcms2-2:armhf (2.12~rc1-2) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../020-libjpeg62-turbo_1%3a2.0.6-4_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.0.6-4) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../021-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../022-libpng16-16_1.6.37-3_armhf.deb ... Unpacking libpng16-16:armhf (1.6.37-3) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../023-libfreetype6_2.10.4+dfsg-1_armhf.deb ... Unpacking libfreetype6:armhf (2.10.4+dfsg-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../024-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../025-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../026-libfontconfig1_2.13.1-4.2_armhf.deb ... Unpacking libfontconfig1:armhf (2.13.1-4.2) ... 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:armhf. Preparing to unpack .../028-libasound2_1.2.4-1.1_armhf.deb ... Unpacking libasound2:armhf (1.2.4-1.1) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../029-libglib2.0-0_2.66.8-1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.66.8-1) ... Selecting previously unselected package libgraphite2-3:armhf. Preparing to unpack .../030-libgraphite2-3_1.3.14-1_armhf.deb ... Unpacking libgraphite2-3:armhf (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:armhf. Preparing to unpack .../031-libharfbuzz0b_2.7.4-1_armhf.deb ... Unpacking libharfbuzz0b:armhf (2.7.4-1) ... Selecting previously unselected package libpcsclite1:armhf. Preparing to unpack .../032-libpcsclite1_1.9.1-1_armhf.deb ... Unpacking libpcsclite1:armhf (1.9.1-1) ... Selecting previously unselected package openjdk-11-jre-headless:armhf. Preparing to unpack .../033-openjdk-11-jre-headless_11.0.12+7-2_armhf.deb ... Unpacking openjdk-11-jre-headless:armhf (11.0.12+7-2) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../034-default-jre-headless_2%3a1.11-72_armhf.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:armhf. Preparing to unpack .../038-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../039-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../040-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../041-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../042-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../043-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../044-dctrl-tools_2.24-3_armhf.deb ... Unpacking dctrl-tools (2.24-3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../045-libdebhelper-perl_13.3.4_all.deb ... 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_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../051-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../052-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../053-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../054-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../055-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. 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Setting up libdevel-callchecker-perl (0.008-1+b2) ... 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:armhf (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 (1.12.0-1) ... 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:armhf (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:armhf (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:armhf (3.9.2-1) ... Setting up libpython3-stdlib:armhf (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:armhf (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:armhf (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:armhf (11.0.12+7-2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jdk-headless:armhf (11.0.12+7-2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jdk-headless (2:1.11-72) ... Setting up devscripts (2.21.3) ... 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:USERTrust_RSA_Certification_Authority.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Certigna_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:TrustCor_ECA-1.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:ISRG_Root_X1.pem Adding debian:ACCVRAIZ1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:GTS_Root_R2.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:SecureTrust_CA.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:GTS_Root_R4.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Secure_Global_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Izenpe.com.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:Certigna.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:GTS_Root_R1.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.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 (2.31-13) ... 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-3.1_source.changes 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 armhf 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: 9 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: 29 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: 5 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: 9 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: 7 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: 9 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: 5 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: 31 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: 17 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: 7 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: 6 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: 5 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: 9 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 10 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 11.0.12 [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: 0.165 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.165 sec [junit] [junit] Testcase: testGetIndexOf took 0.075 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 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 0.001 sec [junit] Testcase: testToString took 0.004 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 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.004 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.005 sec [junit] Testcase: testGetOriginalSequence took 0 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 0.001 sec [junit] Testcase: testGetCompoundSet took 0.001 sec [junit] Testcase: testGetLocationInAlignment took 0.002 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 0.004 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: 0.376 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.376 sec [junit] [junit] Testcase: testGetIndexOf took 0.134 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.004 sec [junit] Testcase: testGetAlignedSequenceInt took 0.004 sec [junit] Testcase: testToStringInt took 0.022 sec [junit] Testcase: testToString took 0.003 sec [junit] Testcase: testToStringFormatted took 0.062 sec [junit] Testcase: testSimpleProfile took 0.001 sec [junit] Testcase: testGetSize took 0 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec [junit] Testcase: testGetAlignedSequences took 0.002 sec [junit] Testcase: testGetOriginalSequences took 0 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0.001 sec [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec [junit] Testcase: testGetIndicesAt took 0.016 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.008 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 0.001 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundSet took 0.001 sec [junit] Testcase: testGetCompoundsAt took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec [junit] Testcase: testIterator took 0.001 sec [junit] Testcase: testGetLastIndexOf took 0.002 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 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: 0.18 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.114 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetCompoundInQueryAt took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.003 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumIdenticals took 0.001 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 0.001 sec [junit] Testcase: testGetIndexInQueryAt took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumSimilars took 0.003 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetAlignment took 0.14 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: 0.69 sec [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.69 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] Aug 13, 2021 10:45:46 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Aug 13, 2021 10:45:46 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 0.357 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 0.244 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0.009 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: 20 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 11.0.12 [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: 0.206 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 sec [junit] [junit] Testcase: testGetQuery took 0.122 sec [junit] Testcase: testGetScore took 0.051 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.002 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.002 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: 0.183 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec [junit] [junit] Testcase: testGetQuery took 0.099 sec [junit] Testcase: testGetScore took 0.048 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.003 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.003 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: 0.35 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 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 0.244 sec [junit] Testcase: testToString took 0.006 sec [junit] Testcase: testGetScoreMatrix took 0.01 sec [junit] Testcase: testGetRoot took 0.044 sec [junit] Testcase: testGetSequences took 0.006 sec [junit] Testcase: testGetDistanceMatrix took 0.005 sec [junit] Testcase: testGetAllPairsScores took 0.006 sec [junit] Testcase: testIterator took 0.005 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: 0.194 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 sec [junit] [junit] Testcase: shouldAllowZeroLengthMatches took 0.174 sec [junit] Running org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.589 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.589 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.099 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.047 sec [junit] Testcase: should_align_middle_anchor took 0.064 sec [junit] Testcase: testGetQuery took 0.005 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec [junit] Testcase: should_align_all_anchored took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.002 sec [junit] Testcase: should_align_multiple_anchors took 0.001 sec [junit] Testcase: testAnchoredDNAAlignment took 0.005 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: should_align_ending_anchor took 0.002 sec [junit] Testcase: testIsStoringScoreMatrix took 0.004 sec [junit] Testcase: testComplex took 0.033 sec [junit] Testcase: testGetScoreMatrixAsString took 0.027 sec [junit] Testcase: should_align_starting_anchor took 0.002 sec [junit] Testcase: anchors_should_not_change_score took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Testcase: testIntOverflowBug took 0.254 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: 0.029 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] [junit] Testcase: testOpenPenalty took 0.007 sec [junit] Testcase: testType took 0 sec [junit] Testcase: testExtensionPenalty took 0 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec [junit] Testcase: testSimpleGapPenalty took 0 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec [junit] [junit] Testcase: testGetQuery took 0.15 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testSimpleProfilePair took 0.009 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: 0.315 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.155 sec [junit] Testcase: testGetGapPenalty took 0.008 sec [junit] Testcase: testGetComputationTime took 0.006 sec [junit] Testcase: testGetQuery took 0.006 sec [junit] Testcase: testGetScore took 0.007 sec [junit] Testcase: testGetScoreMatrix took 0.011 sec [junit] Testcase: testGetPair took 0.011 sec [junit] Testcase: testGetProfile took 0.006 sec [junit] Testcase: testGetMinScore took 0.003 sec [junit] Testcase: testIsStoringScoreMatrix took 0.004 sec [junit] Testcase: testGetScoreMatrixAsString took 0.055 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.003 sec [junit] Testcase: testSimpleProfileProfileAligner took 0.004 sec [junit] Testcase: testGetTarget took 0.004 sec [junit] Testcase: testGetMaxScore took 0.003 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.181 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.181 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.013 sec [junit] Testcase: testSetDescription took 0.029 sec [junit] Testcase: testToString took 0.051 sec [junit] Testcase: testCaseEquivalence took 0.002 sec [junit] Testcase: test took 0.019 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.021 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.005 sec [junit] Testcase: testSetName took 0.013 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: 0.274 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.274 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.097 sec [junit] Testcase: testGetGapPenalty took 0.001 sec [junit] Testcase: testGetComputationTime took 0.047 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.004 sec [junit] Testcase: testGetScoreMatrix took 0.003 sec [junit] Testcase: testGetPair took 0.011 sec [junit] Testcase: testSmithWaterman took 0.003 sec [junit] Testcase: testGetProfile took 0.004 sec [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.057 sec [junit] Testcase: testSetStoringScoreMatrix took 0.011 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.002 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: 0.038 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec [junit] [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.009 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.004 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0.001 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0.001 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0 sec [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.248 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.248 sec [junit] [junit] Testcase: testGetComputationTime took 0.14 sec [junit] Testcase: testGuanUberbacher took 0.002 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testGetPair took 0.009 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: should_align_shorter_target took 0.061 sec [junit] Testcase: should_align_multiple_cuts took 0.003 sec [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Testcase: should_align_shorter_query took 0.001 sec BUILD SUCCESSFUL Total time: 22 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 11.0.12 [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: 1.228 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.228 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 1.075 sec [junit] Testcase: testExample1 took 0.052 sec [junit] Testcase: testExample2 took 0.021 sec [junit] Testcase: testExample3 took 0.008 sec [junit] Testcase: testExample1WithCSV took 0.04 sec [junit] Testcase: testWithCases took 0.007 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: 1.052 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.052 sec [junit] [junit] Testcase: shortExample1 took 0.088 sec [junit] Testcase: shortExample2 took 0.776 sec [junit] Testcase: shortExample3 took 0.144 sec [junit] Testcase: shortExample4 took 0.004 sec [junit] Testcase: shortExample5 took 0.019 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: 1.202 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.202 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testAdvancedXMLExample took 0.982 sec [junit] Testcase: testExample1 took 0.063 sec [junit] Testcase: testExample2 took 0.036 sec [junit] Testcase: testExample3 took 0.028 sec [junit] Testcase: testExample1WithCSV took 0.042 sec [junit] Testcase: testWithCases took 0.027 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: 1.758 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.758 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 0.095 sec [junit] Testcase: testMolecularWeightXMLSingleFile took 0.902 sec [junit] Testcase: testEnrichment took 0.032 sec [junit] Testcase: testApliphaticIndex took 0.004 sec [junit] Testcase: testMolecularWeightXMLNull took 0.011 sec [junit] Testcase: testApliphaticIndexNull took 0.001 sec [junit] Testcase: testIsoelectricPointExpasy took 0.057 sec [junit] Testcase: testAbsorbanceNull took 0.001 sec [junit] Testcase: testIsoelectricPointNull took 0.001 sec [junit] Testcase: testAverageHydropathy took 0.001 sec [junit] Testcase: testExtinctionCoefficient took 0.002 sec [junit] Testcase: testAAComposition took 0.002 sec [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.11 sec [junit] Testcase: testMolecularWeight took 0.002 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.013 sec [junit] Testcase: testNetChargeNull took 0.002 sec [junit] Testcase: testExtinctionCoefficientNull took 0.001 sec [junit] Testcase: testNetCharge took 0.262 sec [junit] Testcase: testEnrichmentNull took 0.001 sec [junit] Testcase: testInstabilityIndexNull took 0.001 sec [junit] Testcase: testAverageHydropathyNull took 0.001 sec [junit] Testcase: testMolecularWeightXML took 0.227 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: 0.025 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] [junit] Testcase: testFake took 0.005 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: 0.056 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] [junit] Testcase: testFakeTest took 0.037 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: 1.258 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.258 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 0.689 sec [junit] Testcase: readWithIDXml took 0.227 sec [junit] Testcase: readMinXml took 0.086 sec [junit] Testcase: readAdvancedXml took 0.053 sec [junit] Testcase: generateXml took 0.045 sec [junit] Testcase: readXml took 0.136 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: 1.104 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.104 sec [junit] [junit] Testcase: generateSchema took 0.721 sec [junit] Testcase: generateXml took 0.106 sec [junit] Testcase: readXml took 0.256 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: 0.056 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] [junit] Testcase: testFake took 0.037 sec BUILD SUCCESSFUL Total time: 23 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 11.0.12 BUILD SUCCESSFUL Total time: 4 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 11.0.12 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.266 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.266 sec [junit] [junit] Testcase: testConvert took 0.239 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: 0.046 sec [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec [junit] [junit] Testcase: testBuildAppendSequence took 0.008 sec [junit] Testcase: testBuildNullDescription took 0 sec [junit] Testcase: testBuildAppendQuality took 0 sec [junit] Testcase: testBuild took 0.002 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 0.001 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 0.001 sec [junit] Testcase: testBuildDefault took 0 sec [junit] Testcase: testBuildMissingSequence took 0 sec [junit] Testcase: testBuildNullQuality took 0 sec [junit] Testcase: testBuildMultiple took 0.001 sec [junit] Testcase: testConstructor took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec [junit] [junit] Testcase: testImmutable took 0.004 sec [junit] Testcase: testBuilder took 0.005 sec [junit] Testcase: testVariant took 0 sec [junit] Testcase: testQuality took 0.003 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0.001 sec [junit] Testcase: testDescription took 0 sec [junit] Testcase: testConstructor took 0.001 sec [junit] Testcase: testSequence took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 sec [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 sec [junit] [junit] Testcase: testErrorProbabilitiesNullFastq took 0.004 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.002 sec [junit] Testcase: testConvertNullVariant took 0 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.002 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.093 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec [junit] Testcase: testCreateQualityScores took 0.001 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec [junit] Testcase: testConvertQualitiesNullFastq took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0.001 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.003 sec [junit] Testcase: testConvertQualitiesNullVariant took 0.001 sec [junit] Testcase: testConvertSameVariant took 0 sec [junit] Testcase: testQualityScores took 0.007 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 0.001 sec [junit] Testcase: testQualityScoresIntArray took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testToList took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec [junit] Testcase: testErrorProbabilities took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec [junit] [junit] Testcase: testParseFastqVariant took 0.007 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0.001 sec [junit] Testcase: testIsSanger took 0.004 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: 0.265 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec [junit] [junit] Testcase: testFullRangeAsIllumina took 0.065 sec [junit] Testcase: testWrappingAsIllumina took 0.006 sec [junit] Testcase: testValidateDescription took 0.016 sec [junit] Testcase: testValidateRepeatDescription took 0.006 sec [junit] Testcase: testMiscDnaAsIllumina took 0.004 sec [junit] Testcase: testMiscRnaAsIllumina took 0.005 sec [junit] Testcase: testLongReadsAsIllumina took 0.007 sec [junit] Testcase: testParseNullReadable took 0.002 sec [junit] Testcase: testReadRoundTripSingleFile took 0.042 sec [junit] Testcase: testReadEmptyFile took 0.001 sec [junit] Testcase: testErrorExamples took 0.061 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.003 sec [junit] Testcase: testReadEmptyInputStream took 0.003 sec [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.003 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.002 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: 0.089 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.014 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec [junit] Testcase: testWriteFileIterable took 0.036 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.003 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: 0.288 sec [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 sec [junit] [junit] Testcase: testMiscRnaAsSanger took 0.065 sec [junit] Testcase: testFullRangeAsSanger took 0.006 sec [junit] Testcase: testWrappingOriginal took 0.006 sec [junit] Testcase: testLongReadsOriginal took 0.01 sec [junit] Testcase: testMiscDnaOriginal took 0.005 sec [junit] Testcase: testMiscRnaOriginal took 0.005 sec [junit] Testcase: testValidateDescription took 0.016 sec [junit] Testcase: testValidateRepeatDescription took 0.004 sec [junit] Testcase: testFullRangeOriginal took 0.004 sec [junit] Testcase: testWrappingAsSanger took 0.004 sec [junit] Testcase: testLongReadsAsSanger took 0.006 sec [junit] Testcase: testMiscDnaAsSanger took 0.003 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.04 sec [junit] Testcase: testReadEmptyFile took 0.001 sec [junit] Testcase: testErrorExamples took 0.058 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.002 sec [junit] Testcase: testReadEmptyInputStream took 0.002 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.003 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.003 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: 0.088 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] [junit] Testcase: testConvertNotSangerVariant took 0.015 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec [junit] Testcase: testWriteFileIterable took 0.036 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.003 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: 0.265 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec [junit] [junit] Testcase: testMiscRnaAsSolexa took 0.065 sec [junit] Testcase: testFullRangeAsSolexa took 0.005 sec [junit] Testcase: testValidateDescription took 0.016 sec [junit] Testcase: testValidateRepeatDescription took 0.006 sec [junit] Testcase: testWrappingAsSolexa took 0.005 sec [junit] Testcase: testLongReadsAsSolexa took 0.008 sec [junit] Testcase: testMiscDnaAsSolexa took 0.003 sec [junit] Testcase: testParseNullReadable took 0.002 sec [junit] Testcase: testReadRoundTripSingleFile took 0.043 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.059 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.003 sec [junit] Testcase: testReadEmptyInputStream took 0.003 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.003 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 0.001 sec [junit] Testcase: testWrappedQuality took 0.003 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: 0.088 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] [junit] Testcase: testConvertNotSolexaVariant took 0.015 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec [junit] Testcase: testWriteFileIterable took 0.036 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.003 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: 0.036 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec [junit] [junit] Testcase: testStreamNullVariant took 0.004 sec [junit] Testcase: testStreamNullListener took 0.005 sec [junit] Testcase: testStreamNullReadable took 0.002 sec BUILD SUCCESSFUL Total time: 18 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 11.0.12 [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: 0.025 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] [junit] Testcase: testMe took 0.002 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: 0.025 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] [junit] Testcase: testSomeMethod took 0.002 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: 0.037 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec [junit] [junit] Testcase: testGetColor took 0.005 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec [junit] Testcase: testGetSelection took 0.004 sec [junit] Testcase: testRepaint took 0.001 sec [junit] Testcase: testSetSelection took 0 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec [junit] Testcase: testSetStyle took 0 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: 0.026 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL Total time: 8 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 11.0.12 BUILD SUCCESSFUL Total time: 4 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 322289457 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_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload 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/21715 and its subdirectories I: Current time: Fri Aug 13 10:48:09 -12 2021 I: pbuilder-time-stamp: 1628894889 Fri Aug 13 22:49:03 UTC 2021 I: 1st build successful. Starting 2nd build on remote node virt32a-armhf-rb.debian.net. Fri Aug 13 22:49:03 UTC 2021 I: Preparing to do remote build '2' on virt32a-armhf-rb.debian.net. Fri Aug 13 23:00:12 UTC 2021 I: Deleting $TMPDIR on virt32a-armhf-rb.debian.net. Fri Aug 13 23:00:14 UTC 2021 I: biojava4-live_4.2.12+dfsg-3.1_armhf.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: da166b47f1fdc72050a127c80ff59662210fc3e5 11715 biojava4-live_4.2.12+dfsg-3.1_armhf.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 ecda98e447268b4fd5cc96328576ccd062994072 5451996 libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb Checksums-Sha256: 6ea17b89705063a81daa9715c9926424a4144ebb2f58cf63463879d799b755a9 11715 biojava4-live_4.2.12+dfsg-3.1_armhf.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 9b8730b872e9c5e0c95bafce6c030bdc7b1cff387dcfb64d01833dd7c7f09727 5451996 libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb Files: f64c451835d370881dd24429cf8fc0b4 11715 java optional biojava4-live_4.2.12+dfsg-3.1_armhf.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 abb0e37f042b3b2080b111705510a2bf 5451996 java optional libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb Fri Aug 13 23:00:16 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/biojava4-live_4.2.12+dfsg-3.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/biojava4-live_4.2.12+dfsg-3.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/biojava4-live_4.2.12+dfsg-3.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/b1/biojava4-live_4.2.12+dfsg-3.1_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/b2/biojava4-live_4.2.12+dfsg-3.1_armhf.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: 1.293s) 1.293s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.806s) 0.806s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Aug 13 23:38:23 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 13 23:38:23 UTC 2021 I: biojava4-live from bullseye built successfully and reproducibly on armhf. Fri Aug 13 23:38:28 UTC 2021 I: Submitting .buildinfo files to external archives: Fri Aug 13 23:38:28 UTC 2021 I: Submitting 16K b1/biojava4-live_4.2.12+dfsg-3.1_armhf.buildinfo.asc Fri Aug 13 23:38:29 UTC 2021 I: Submitting 16K b2/biojava4-live_4.2.12+dfsg-3.1_armhf.buildinfo.asc Fri Aug 13 23:38:30 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Aug 13 23:38:30 UTC 2021 I: Done submitting .buildinfo files. Fri Aug 13 23:38:30 UTC 2021 I: Removing signed biojava4-live_4.2.12+dfsg-3.1_armhf.buildinfo.asc files: removed './b1/biojava4-live_4.2.12+dfsg-3.1_armhf.buildinfo.asc' removed './b2/biojava4-live_4.2.12+dfsg-3.1_armhf.buildinfo.asc'