RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux allspice 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 Buildd toolchain package versions: launchpad-buildd_121~0.IS.08.04.0 python-lpbuildd_121~0.IS.08.04.0 bzr_2.5.1-0ubuntu2 dpkg-dev_1.16.1.2ubuntu7.2. Syncing the system clock with the buildd NTP service... 3 Feb 17:11:50 ntpdate[30084]: adjust time server 10.211.37.1 offset -0.000036 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5549150', '/home/buildd/filecache-default/85437d411726979c3d865ddb70b8896a411f3906'] Unpacking chroot for build PACKAGEBUILD-5549150 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5549150'] Mounting chroot for build PACKAGEBUILD-5549150 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5549150', 'deb http://ftpmaster.internal/ubuntu trusty main universe', 'deb http://ftpmaster.internal/ubuntu trusty-security main universe', 'deb http://ftpmaster.internal/ubuntu trusty-updates main universe', 'deb http://ftpmaster.internal/ubuntu trusty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-5549150 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5549150', 'i386'] Updating debian chroot for build PACKAGEBUILD-5549150 Ign http://ftpmaster.internal trusty InRelease Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty-security InRelease Ign http://archive-team.internal trusty Release.gpg Ign http://ftpmaster.internal trusty-updates InRelease Get:1 http://archive-team.internal trusty Release [723 B] Ign http://ftpmaster.internal trusty-proposed InRelease Get:2 http://ftpmaster.internal trusty Release.gpg [933 B] Get:3 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:4 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal trusty Release [58.5 kB] Get:7 http://archive-team.internal trusty/main i386 Packages Get:8 http://ftpmaster.internal trusty-security Release [58.5 kB] Get:9 http://ftpmaster.internal trusty-updates Release [58.5 kB] Ign http://archive-team.internal trusty/main Translation-en Get:10 http://ftpmaster.internal trusty-proposed Release [58.5 kB] Get:11 http://ftpmaster.internal trusty/main i386 Packages [1319 kB] Get:12 http://ftpmaster.internal trusty/universe i386 Packages [5877 kB] Get:13 http://ftpmaster.internal trusty/main Translation-en [751 kB] Get:14 http://ftpmaster.internal trusty/universe Translation-en [4051 kB] Get:15 http://ftpmaster.internal trusty-security/main i386 Packages [14 B] Get:16 http://ftpmaster.internal trusty-security/universe i386 Packages [14 B] Get:17 http://ftpmaster.internal trusty-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal trusty-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal trusty-updates/main i386 Packages [14 B] Get:20 http://ftpmaster.internal trusty-updates/universe i386 Packages [14 B] Get:21 http://ftpmaster.internal trusty-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal trusty-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal trusty-proposed/main i386 Packages [56.4 kB] Get:24 http://ftpmaster.internal trusty-proposed/universe i386 Packages [120 kB] Get:25 http://ftpmaster.internal trusty-proposed/main Translation-en [27.8 kB] Get:26 http://ftpmaster.internal trusty-proposed/universe Translation-en [80.4 kB] Fetched 12.5 MB in 6s (2023 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libprocps1 Use 'apt-get autoremove' to remove it. The following NEW packages will be installed: libdebconfclient0 libprocps3 The following packages will be upgraded: apt apt-transport-https base-files base-passwd binutils bsdutils cpp cpp-4.8 dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-4.8 gcc gcc-4.8 gcc-4.8-base gnupg gpgv grep gzip ifupdown libapt-pkg4.12 libasan0 libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcomerr2 libcurl3-gnutls libdbus-1-3 libdpkg-perl libdrm2 libffi6 libgcc-4.8-dev libgcc1 libgmp10 libgomp1 libitm1 libmount1 libncurses5 libncursesw5 libpam-modules libpam-modules-bin libpam-runtime libpam0g libquadmath0 libselinux1 libsqlite3-0 libss2 libstdc++-4.8-dev libstdc++6 libtinfo5 libudev1 libuuid1 linux-libc-dev login mount multiarch-support ncurses-base ncurses-bin passwd perl perl-base perl-modules pkgbinarymangler procps udev upstart util-linux 73 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 45.9 MB of archives. After this operation, 2301 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main base-files i386 7.2ubuntu1 [45.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main dpkg i386 1.17.5ubuntu2 [1944 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main libc-bin i386 2.18-0ubuntu6 [1100 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libdbus-1-3 i386 1.6.18-0ubuntu3 [131 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main libselinux1 i386 2.2.2-1 [56.6 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main libpam0g i386 1.1.8-1ubuntu2 [55.1 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libpam-modules-bin i386 1.1.8-1ubuntu2 [30.8 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main libpam-modules i386 1.1.8-1ubuntu2 [232 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main passwd i386 1:4.1.5.1-1ubuntu8 [746 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main libuuid1 i386 2.20.1-5.1ubuntu14 [11.5 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libblkid1 i386 2.20.1-5.1ubuntu14 [67.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main util-linux i386 2.20.1-5.1ubuntu14 [450 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libprocps3 i386 1:3.3.9-1ubuntu2 [30.0 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libncursesw5 i386 5.9+20131221-1ubuntu1 [122 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main libtinfo5 i386 5.9+20131221-1ubuntu1 [70.9 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libncurses5 i386 5.9+20131221-1ubuntu1 [93.7 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main procps i386 1:3.3.9-1ubuntu2 [203 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main udev i386 204-5ubuntu10 [736 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main libudev1 i386 204-5ubuntu10 [36.2 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main ifupdown i386 0.7.47.2ubuntu1 [51.3 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main upstart i386 1.11-0ubuntu2 [364 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main libc6-dev i386 2.18-0ubuntu6 [2552 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libc-dev-bin i386 2.18-0ubuntu6 [63.4 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main linux-libc-dev i386 3.13.0-6.23 [761 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main libitm1 i386 4.8.2-14ubuntu4 [28.4 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main libgomp1 i386 4.8.2-14ubuntu4 [25.0 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main libasan0 i386 4.8.2-14ubuntu4 [64.0 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8-base i386 4.8.2-14ubuntu4 [15.1 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main libgcc1 i386 1:4.8.2-14ubuntu4 [46.5 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main libatomic1 i386 4.8.2-14ubuntu4 [8228 B] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main libquadmath0 i386 4.8.2-14ubuntu4 [187 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main cpp-4.8 i386 4.8.2-14ubuntu4 [4448 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++-4.8-dev i386 4.8.2-14ubuntu4 [1043 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main g++-4.8 i386 4.8.2-14ubuntu4 [4811 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8 i386 4.8.2-14ubuntu4 [4867 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main libgcc-4.8-dev i386 4.8.2-14ubuntu4 [1735 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++6 i386 4.8.2-14ubuntu4 [261 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main libgmp10 i386 2:5.1.3+dfsg-1ubuntu1 [230 kB] Get:39 http://ftpmaster.internal/ubuntu/ trusty/main binutils i386 2.24-2ubuntu3 [2109 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main libc6 i386 2.18-0ubuntu6 [4017 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main e2fslibs i386 1.42.9-2ubuntu1 [192 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main e2fsprogs i386 1.42.9-2ubuntu1 [665 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty/main findutils i386 4.4.2-7 [237 kB] Get:44 http://ftpmaster.internal/ubuntu/ trusty/main grep i386 2.16-1 [157 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty/main gzip i386 1.6-3ubuntu1 [83.8 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty/main login i386 1:4.1.5.1-1ubuntu8 [302 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty/main mount i386 2.20.1-5.1ubuntu14 [113 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty/main ncurses-bin i386 5.9+20131221-1ubuntu1 [135 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/main perl i386 5.18.2-2 [2159 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty/main perl-base i386 5.18.2-2 [1133 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty/main perl-modules all 5.18.2-2 [2696 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty/main libapt-pkg4.12 i386 0.9.14.1ubuntu2 [623 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty/main gpgv i386 1.4.16-1ubuntu1 [152 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main gnupg i386 1.4.16-1ubuntu1 [593 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty/main apt i386 0.9.14.1ubuntu2 [954 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty/main libdebconfclient0 i386 0.187ubuntu1 [6594 B] Get:57 http://ftpmaster.internal/ubuntu/ trusty/main base-passwd i386 3.5.32 [45.6 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty/main bsdutils i386 1:2.20.1-5.1ubuntu14 [34.1 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty/main ncurses-base all 5.9+20131221-1ubuntu1 [16.5 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty/main libcomerr2 i386 1.42.9-2ubuntu1 [62.4 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty/main libmount1 i386 2.20.1-5.1ubuntu14 [59.7 kB] Get:62 http://ftpmaster.internal/ubuntu/ trusty/main libss2 i386 1.42.9-2ubuntu1 [66.5 kB] Get:63 http://ftpmaster.internal/ubuntu/ trusty/main libffi6 i386 3.0.13-12 [14.3 kB] Get:64 http://ftpmaster.internal/ubuntu/ trusty/main libsqlite3-0 i386 3.8.2-1ubuntu2 [344 kB] Get:65 http://ftpmaster.internal/ubuntu/ trusty/main libdrm2 i386 2.4.52-1 [23.2 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty/main libcurl3-gnutls i386 7.35.0-1ubuntu1 [166 kB] Get:67 http://ftpmaster.internal/ubuntu/ trusty/main libpam-runtime all 1.1.8-1ubuntu2 [37.7 kB] Get:68 http://ftpmaster.internal/ubuntu/ trusty/main multiarch-support i386 2.18-0ubuntu6 [4486 B] Get:69 http://ftpmaster.internal/ubuntu/ trusty/main apt-transport-https i386 0.9.14.1ubuntu2 [24.9 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty/main cpp i386 4:4.8.2-1ubuntu3 [27.7 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty/main dpkg-dev all 1.17.5ubuntu2 [726 kB] Get:72 http://ftpmaster.internal/ubuntu/ trusty/main libdpkg-perl all 1.17.5ubuntu2 [179 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty/main gcc i386 4:4.8.2-1ubuntu3 [4990 B] Get:74 http://ftpmaster.internal/ubuntu/ trusty/main g++ i386 4:4.8.2-1ubuntu3 [1492 B] Get:75 http://ftpmaster.internal/ubuntu/ trusty/main pkgbinarymangler all 119 [28.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.9 MB in 5s (8320 kB/s) (Reading database ... 11989 files and directories currently installed.) Preparing to replace base-files 6.12ubuntu5 (using .../base-files_7.2ubuntu1_i386.deb) ... Unpacking replacement base-files ... Setting up base-files (7.2ubuntu1) ... Installing new version of config file /etc/debian_version ... (Reading database ... 11989 files and directories currently installed.) Preparing to replace dpkg 1.17.1ubuntu1 (using .../dpkg_1.17.5ubuntu2_i386.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.17.5ubuntu2) ... (Reading database ... 11991 files and directories currently installed.) Preparing to unpack .../libc-bin_2.18-0ubuntu6_i386.deb ... Unpacking libc-bin (2.18-0ubuntu6) over (2.18-0ubuntu2) ... Preparing to unpack .../libc6_2.18-0ubuntu6_i386.deb ... Unpacking libc6:i386 (2.18-0ubuntu6) over (2.18-0ubuntu2) ... Preparing to unpack .../libgcc1_1%3a4.8.2-14ubuntu4_i386.deb ... Unpacking libgcc1:i386 (1:4.8.2-14ubuntu4) over (1:4.8.2-10ubuntu2) ... Preparing to unpack .../gcc-4.8-base_4.8.2-14ubuntu4_i386.deb ... Unpacking gcc-4.8-base:i386 (4.8.2-14ubuntu4) over (4.8.2-10ubuntu2) ... Setting up gcc-4.8-base:i386 (4.8.2-14ubuntu4) ... Setting up libgcc1:i386 (1:4.8.2-14ubuntu4) ... Setting up libc6:i386 (2.18-0ubuntu6) ... Setting up libc-bin (2.18-0ubuntu6) ... (Reading database ... 11991 files and directories currently installed.) Preparing to unpack .../libdbus-1-3_1.6.18-0ubuntu3_i386.deb ... Unpacking libdbus-1-3:i386 (1.6.18-0ubuntu3) over (1.6.18-0ubuntu2) ... Preparing to unpack .../libselinux1_2.2.2-1_i386.deb ... Unpacking libselinux1:i386 (2.2.2-1) over (2.2.1-1ubuntu2) ... Setting up libselinux1:i386 (2.2.2-1) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... (Reading database ... 11991 files and directories currently installed.) Preparing to unpack .../libpam0g_1.1.8-1ubuntu2_i386.deb ... Unpacking libpam0g:i386 (1.1.8-1ubuntu2) over (1.1.3-10ubuntu1) ... Setting up libpam0g:i386 (1.1.8-1ubuntu2) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... 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Unpacking util-linux (2.20.1-5.1ubuntu14) over (2.20.1-5.1ubuntu11) ... Setting up util-linux (2.20.1-5.1ubuntu14) ... Installing new version of config file /etc/cron.weekly/fstrim ... Selecting previously unselected package libprocps3:i386. (Reading database ... 11992 files and directories currently installed.) Preparing to unpack .../libprocps3_1%3a3.3.9-1ubuntu2_i386.deb ... Unpacking libprocps3:i386 (1:3.3.9-1ubuntu2) ... Preparing to unpack .../libncursesw5_5.9+20131221-1ubuntu1_i386.deb ... Unpacking libncursesw5:i386 (5.9+20131221-1ubuntu1) over (5.9+20130608-1ubuntu1) ... Preparing to unpack .../libtinfo5_5.9+20131221-1ubuntu1_i386.deb ... Unpacking libtinfo5:i386 (5.9+20131221-1ubuntu1) over (5.9+20130608-1ubuntu1) ... Setting up libtinfo5:i386 (5.9+20131221-1ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... (Reading database ... 11998 files and directories currently installed.) Preparing to unpack .../libncurses5_5.9+20131221-1ubuntu1_i386.deb ... 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Changing shell of daemon from /bin/sh to /usr/sbin/nologin Changing shell of bin from /bin/sh to /usr/sbin/nologin Changing shell of sys from /bin/sh to /usr/sbin/nologin Changing shell of games from /bin/sh to /usr/sbin/nologin Changing shell of man from /bin/sh to /usr/sbin/nologin Changing shell of lp from /bin/sh to /usr/sbin/nologin Changing shell of mail from /bin/sh to /usr/sbin/nologin Changing shell of news from /bin/sh to /usr/sbin/nologin Changing shell of uucp from /bin/sh to /usr/sbin/nologin Changing shell of proxy from /bin/sh to /usr/sbin/nologin Changing shell of www-data from /bin/sh to /usr/sbin/nologin Changing shell of backup from /bin/sh to /usr/sbin/nologin Changing shell of list from /bin/sh to /usr/sbin/nologin Changing shell of irc from /bin/sh to /usr/sbin/nologin Changing shell of gnats from /bin/sh to /usr/sbin/nologin Changing shell of nobody from /bin/sh to /usr/sbin/nologin 16 changes have been made, rewriting files Writing passwd-file to /etc/passwd Writing shadow-file to /etc/shadow Writing group-file to /etc/group (Reading database ... 12004 files and directories currently installed.) 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Unpacking libdpkg-perl (1.17.5ubuntu2) over (1.17.1ubuntu1) ... Preparing to unpack .../gcc_4%3a4.8.2-1ubuntu3_i386.deb ... Removing old gcc doc directory. Unpacking gcc (4:4.8.2-1ubuntu3) over (4:4.8.2-1ubuntu2) ... Preparing to unpack .../g++_4%3a4.8.2-1ubuntu3_i386.deb ... Unpacking g++ (4:4.8.2-1ubuntu3) over (4:4.8.2-1ubuntu2) ... Preparing to unpack .../pkgbinarymangler_119_all.deb ... Unpacking pkgbinarymangler (119) over (118) ... Setting up libdbus-1-3:i386 (1.6.18-0ubuntu3) ... Setting up libprocps3:i386 (1:3.3.9-1ubuntu2) ... Setting up libncursesw5:i386 (5.9+20131221-1ubuntu1) ... Setting up procps (1:3.3.9-1ubuntu2) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libudev1:i386 (204-5ubuntu10) ... Setting up udev (204-5ubuntu10) ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up ifupdown (0.7.47.2ubuntu1) ... Setting up upstart (1.11-0ubuntu2) ... Setting up libc-dev-bin (2.18-0ubuntu6) ... Setting up linux-libc-dev:i386 (3.13.0-6.23) ... Setting up libc6-dev:i386 (2.18-0ubuntu6) ... Setting up libitm1:i386 (4.8.2-14ubuntu4) ... Setting up libgomp1:i386 (4.8.2-14ubuntu4) ... Setting up libasan0:i386 (4.8.2-14ubuntu4) ... Setting up libatomic1:i386 (4.8.2-14ubuntu4) ... Setting up libquadmath0:i386 (4.8.2-14ubuntu4) ... Setting up libgmp10:i386 (2:5.1.3+dfsg-1ubuntu1) ... Setting up cpp-4.8 (4.8.2-14ubuntu4) ... Setting up libgcc-4.8-dev:i386 (4.8.2-14ubuntu4) ... Setting up libstdc++-4.8-dev:i386 (4.8.2-14ubuntu4) ... Setting up binutils (2.24-2ubuntu3) ... Setting up gcc-4.8 (4.8.2-14ubuntu4) ... Setting up g++-4.8 (4.8.2-14ubuntu4) ... Setting up libffi6:i386 (3.0.13-12) ... Setting up libsqlite3-0:i386 (3.8.2-1ubuntu2) ... Setting up libdrm2:i386 (2.4.52-1) ... Setting up libcurl3-gnutls:i386 (7.35.0-1ubuntu1) ... Setting up apt-transport-https (0.9.14.1ubuntu2) ... Setting up cpp (4:4.8.2-1ubuntu3) ... Setting up gcc (4:4.8.2-1ubuntu3) ... Setting up g++ (4:4.8.2-1ubuntu3) ... Setting up pkgbinarymangler (119) ... Setting up perl-modules (5.18.2-2) ... Setting up perl (5.18.2-2) ... Setting up libdpkg-perl (1.17.5ubuntu2) ... Setting up dpkg-dev (1.17.5ubuntu2) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... Processing triggers for initramfs-tools (0.103ubuntu3) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5549150', 'i386', 'trusty-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty-proposed', '-A', '--purpose=PRIMARY', '--architecture=i386', '--comp=universe', 'biojava3-live_3.0.7+dfsg-1.dsc'] Initiating build PACKAGEBUILD-5549150 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 i686 Automatic build of biojava3-live_3.0.7+dfsg-1 on allspice by sbuild/i386 1.170.5 Build started at 20140203-1712 ****************************************************************************** biojava3-live_3.0.7+dfsg-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), ant Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java, libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1), libcommons-logging-java, libcommons-cli-java, libguava-java (>= 11.0.1), libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java, default-jdk (>= 1:1.6), junit4, javahelper (>= 0.25), ant-optional, icedtea-netx, libhamcrest-java, libjson-simple-java, liblog4j1.2-java Checking for already installed source dependencies... debhelper: missing ant: missing libcommons-dbcp-java: missing libhsqldb-java: missing libcommons-collections-java: missing libcommons-pool-java: missing libcommons-logging-java: missing libcommons-cli-java: missing libguava-java: missing libcommons-codec-java: missing libitext5-java: missing libjmol-java: missing default-jdk: missing junit4: missing javahelper: missing ant-optional: missing icedtea-netx: missing libhamcrest-java: missing libjson-simple-java: missing liblog4j1.2-java: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper ant libcommons-dbcp-java libhsqldb-java libcommons-collections-java libcommons-pool-java libcommons-logging-java libcommons-cli-java libguava-java libcommons-codec-java libitext5-java libjmol-java default-jdk junit4 javahelper ant-optional icedtea-netx libhamcrest-java libjson-simple-java liblog4j1.2-java Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libprocps1 Use 'apt-get autoremove' to remove it. The following extra packages will be installed: apparmor-easyprof bsdmainutils ca-certificates ca-certificates-java dctrl-tools default-jre default-jre-headless devscripts dh-apparmor dh-python file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base icedtea-netx-common intltool-debian java-common libapache-pom-java libarchive-zip-perl libasound2 libasound2-data libasprintf0c2 libasyncns0 libatinject-jsr330-api-java libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcommons-collections3-java libcommons-lang-java libcommons-parent-java libcroco3 libcups2 libdatrie1 libexpat1 libflac8 libfontconfig1 libfreetype6 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgif4 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libjasper1 libjbig0 libjpeg-turbo8 libjpeg8 libjsr305-java liblcms2-2 libmagic1 libmpdec2 libnspr4 libnss3 libnss3-1d libnss3-nssdb libogg0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpipeline1 libpixman-1-0 libpulse0 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libservlet3.0-java libsndfile1 libssl1.0.0 libthai-data libthai0 libtiff5 libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-glx0 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxi6 libxinerama1 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxrandr2 libxrender1 libxtst6 libxxf86vm1 man-db mime-support openjdk-7-jdk openjdk-7-jre openjdk-7-jre-headless openssl po-debconf python3 python3-minimal python3.3 python3.3-minimal shared-mime-info tzdata-java ucf x11-common Suggested packages: ant-doc ant-gcj ant-optional-gcj antlr javacc junit jython libbcel-java libbsf-java libcommons-net-java libgnumail-java libjaxp1.3-java libjdepend-java libjsch-java liboro-java libregexp-java libxalan2-java wamerican wordlist whois vacation debtags dh-make bsd-mailx mailx cvs-buildpackage devscripts-el gnuplot libauthen-sasl-perl libfile-desktopentry-perl libnet-smtp-ssl-perl libterm-size-perl libyaml-syck-perl mutt ssh-client svn-buildpackage w3m debian-keyring equivs liblwp-protocol-https-perl libsoap-lite-perl gettext-doc groff cvs gawk tofrodos libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc libcommons-collections-java-doc libcommons-collections3-java-doc libcommons-dbcp-java-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java cups-common librsvg2-common gvfs java-virtual-machine libhsqldb-java-doc libitext5-java-doc libjasper-runtime libjmol-java-doc libjson-simple-doc libjsr305-java-doc liblcms2-utils liblog4j1.2-java-doc ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp pcscd pulseaudio libxerces2-java-doc libxerces2-java-gcj libxml-commons-resolver1.1-java-doc less www-browser openjdk-7-demo openjdk-7-source visualvm icedtea-7-plugin libnss-mdns sun-java6-fonts fonts-ipafont-gothic fonts-ipafont-mincho ttf-wqy-microhei ttf-wqy-zenhei ttf-indic-fonts-core ttf-telugu-fonts ttf-oriya-fonts ttf-kannada-fonts ttf-bengali-fonts libmail-box-perl python3-doc python3-tk python3.3-doc binfmt-support Recommended packages: at dput dupload libdistro-info-perl libencode-locale-perl libjson-perl libparse-debcontrol-perl liburi-perl libwww-perl lintian patchutils python3-debian python3-magic strace unzip wdiff wget curl libasprintf-dev libgettextpo-dev libgeronimo-jta-1.1-spec-java libgl1-mesa-dri libglib2.0-data hicolor-icon-theme libgtk2.0-bin libbcpkix-java libbcprov-java libxml-security-java tcpd xml-core libxt-dev libgnome2-0 libgnomevfs2-0 libgconf2-4 fonts-dejavu-extra icedtea-7-jre-jamvm libmail-sendmail-perl The following NEW packages will be installed: ant ant-optional apparmor-easyprof bsdmainutils ca-certificates ca-certificates-java dctrl-tools debhelper default-jdk default-jre default-jre-headless devscripts dh-apparmor dh-python file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base icedtea-netx icedtea-netx-common intltool-debian java-common javahelper junit4 libapache-pom-java libarchive-zip-perl libasound2 libasound2-data libasprintf0c2 libasyncns0 libatinject-jsr330-api-java libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcommons-cli-java libcommons-codec-java libcommons-collections-java libcommons-collections3-java libcommons-dbcp-java libcommons-lang-java libcommons-logging-java libcommons-parent-java libcommons-pool-java libcroco3 libcups2 libdatrie1 libexpat1 libflac8 libfontconfig1 libfreetype6 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgif4 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libgtk2.0-0 libgtk2.0-common libguava-java libhamcrest-java libharfbuzz0b libhsqldb-java libitext5-java libjasper1 libjbig0 libjmol-java libjpeg-turbo8 libjpeg8 libjson-simple-java libjsr305-java liblcms2-2 liblog4j1.2-java libmagic1 libmpdec2 libnspr4 libnss3 libnss3-1d libnss3-nssdb libogg0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpipeline1 libpixman-1-0 libpulse0 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libservlet3.0-java libsndfile1 libssl1.0.0 libthai-data libthai0 libtiff5 libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-glx0 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxi6 libxinerama1 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxrandr2 libxrender1 libxtst6 libxxf86vm1 man-db mime-support openjdk-7-jdk openjdk-7-jre openjdk-7-jre-headless openssl po-debconf python3 python3-minimal python3.3 python3.3-minimal shared-mime-info tzdata-java ucf x11-common 0 upgraded, 148 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After this operation, 198 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main libexpat1 i386 2.1.0-4ubuntu1 [71.4 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main libmagic1 i386 1:5.14-2ubuntu1 [184 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main libssl1.0.0 i386 1.0.1f-1ubuntu1 [780 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.3-minimal i386 3.3.4~rc1-1ubuntu1 [396 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main mime-support all 3.54ubuntu1 [31.7 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main libmpdec2 i386 2.4.0-6 [73.3 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.3-stdlib i386 3.3.4~rc1-1ubuntu1 [1959 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main python3.3-minimal i386 3.3.4~rc1-1ubuntu1 [1314 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main libasprintf0c2 i386 0.18.3.1-1ubuntu2 [6618 B] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main libglib2.0-0 i386 2.39.3-0ubuntu4 [1018 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 i386 1.2.6-1 [23.3 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libxau6 i386 1:1.0.8-1 [8352 B] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libxdmcp6 i386 1:1.1.1-1 [13.1 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libxcb1 i386 1.10-2ubuntu1 [40.6 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main libx11-data all 2:1.6.2-1ubuntu2 [111 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libx11-6 i386 2:1.6.2-1ubuntu2 [557 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libxext6 i386 2:1.3.2-1 [33.9 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libxml2 i386 2.9.1+dfsg1-3ubuntu3 [555 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main groff-base i386 1.22.2-5 [1030 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils i386 9.0.5ubuntu1 [197 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main man-db i386 2.6.6-1 [851 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main libasound2-data all 1.0.27.2-3ubuntu1 [30.5 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libasound2 i386 1.0.27.2-3ubuntu1 [407 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main libasyncns0 i386 0.8-4ubuntu2 [11.6 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main libatk1.0-data all 2.10.0-2ubuntu1 [13.8 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main libatk1.0-0 i386 2.10.0-2ubuntu1 [49.5 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main libgtk2.0-common all 2.24.22-1ubuntu1 [121 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main fonts-dejavu-core all 2.34-1ubuntu1 [1024 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main ucf all 3.0027+nmu1 [56.3 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main fontconfig-config all 2.11.0-0ubuntu4 [47.3 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main libfreetype6 i386 2.5.2-1ubuntu1 [300 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main libfontconfig1 i386 2.11.0-0ubuntu4 [123 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main libpixman-1-0 i386 0.30.2-2ubuntu1 [216 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-render0 i386 1.10-2ubuntu1 [11.9 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-shm0 i386 1.10-2ubuntu1 [5622 B] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main libxrender1 i386 1:0.9.8-1 [20.3 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main libcairo2 i386 1.12.16-0ubuntu2 [649 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main libavahi-common-data i386 0.6.31-4ubuntu1 [21.3 kB] Get:39 http://ftpmaster.internal/ubuntu/ trusty/main libavahi-common3 i386 0.6.31-4ubuntu1 [22.2 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main libavahi-client3 i386 0.6.31-4ubuntu1 [24.5 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libcups2 i386 1.7.1-3 [178 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg-turbo8 i386 1.3.0-0ubuntu2 [107 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg8 i386 8c-2ubuntu8 [2188 B] Get:44 http://ftpmaster.internal/ubuntu/ trusty/main libjasper1 i386 1.900.1-14ubuntu3 [126 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty/main libjbig0 i386 2.0-2ubuntu4 [24.9 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty/main libtiff5 i386 4.0.3-7 [143 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty/main libgdk-pixbuf2.0-common all 2.30.3-0ubuntu1 [8620 B] Get:48 http://ftpmaster.internal/ubuntu/ trusty/main libgdk-pixbuf2.0-0 i386 2.30.3-0ubuntu1 [155 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/main libthai-data all 0.1.20-3 [130 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty/main libdatrie1 i386 0.2.8-1 [17.3 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty/main libthai0 i386 0.1.20-3 [17.1 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty/main fontconfig i386 2.11.0-0ubuntu4 [175 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty/main libpango-1.0-0 i386 1.36.1-0ubuntu1 [147 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main libgraphite2-3 i386 1.2.4-1ubuntu1 [54.4 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty/main libharfbuzz0b i386 0.9.25-1ubuntu1 [124 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty/main libpangoft2-1.0-0 i386 1.36.1-0ubuntu1 [32.1 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty/main libpangocairo-1.0-0 i386 1.36.1-0ubuntu1 [19.6 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty/main libxcomposite1 i386 1:0.4.4-1 [7594 B] Get:59 http://ftpmaster.internal/ubuntu/ trusty/main libxfixes3 i386 1:5.0.1-1ubuntu1 [11.5 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty/main libxcursor1 i386 1:1.1.14-1 [22.8 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty/main libxdamage1 i386 1:1.1.4-1ubuntu1 [7406 B] Get:62 http://ftpmaster.internal/ubuntu/ trusty/main libxi6 i386 2:1.7.1.901-1ubuntu1 [32.0 kB] Get:63 http://ftpmaster.internal/ubuntu/ trusty/main libxinerama1 i386 2:1.1.3-1 [7900 B] Get:64 http://ftpmaster.internal/ubuntu/ trusty/main libxrandr2 i386 2:1.4.2-1 [16.1 kB] Get:65 http://ftpmaster.internal/ubuntu/ trusty/main shared-mime-info i386 1.2-0ubuntu1 [413 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty/main libgtk2.0-0 i386 2.24.22-1ubuntu1 [1692 kB] Get:67 http://ftpmaster.internal/ubuntu/ trusty/main openssl i386 1.0.1f-1ubuntu1 [481 kB] Get:68 http://ftpmaster.internal/ubuntu/ trusty/main ca-certificates all 20130906ubuntu1 [180 kB] Get:69 http://ftpmaster.internal/ubuntu/ trusty/main libnspr4 i386 2:4.10.2-1ubuntu1 [111 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty/main libnss3-nssdb all 2:3.15.4-1ubuntu5 [10.6 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty/main libnss3 i386 2:3.15.4-1ubuntu5 [1048 kB] Get:72 http://ftpmaster.internal/ubuntu/ trusty/main ca-certificates-java all 20130815 [13.7 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty/main tzdata-java all 2013i-1 [72.0 kB] Get:74 http://ftpmaster.internal/ubuntu/ trusty/main java-common all 0.48ubuntu3 [129 kB] Get:75 http://ftpmaster.internal/ubuntu/ trusty/main liblcms2-2 i386 2.5-0ubuntu4 [129 kB] Get:76 http://ftpmaster.internal/ubuntu/ trusty/main libnss3-1d i386 2:3.15.4-1ubuntu5 [9296 B] Get:77 http://ftpmaster.internal/ubuntu/ trusty/main libpcsclite1 i386 1.8.10-1ubuntu1 [21.0 kB] Get:78 http://ftpmaster.internal/ubuntu/ trusty/main openjdk-7-jre-headless i386 7u51-2.4.5-1ubuntu1 [41.1 MB] Get:79 http://ftpmaster.internal/ubuntu/ trusty/main default-jre-headless i386 1:1.7-48ubuntu3 [2984 B] Get:80 http://ftpmaster.internal/ubuntu/ trusty/main libgif4 i386 4.1.6-11 [28.4 kB] Get:81 http://ftpmaster.internal/ubuntu/ trusty/main libogg0 i386 1.3.1-1ubuntu1 [16.1 kB] Get:82 http://ftpmaster.internal/ubuntu/ trusty/main libflac8 i386 1.3.0-2 [98.1 kB] Get:83 http://ftpmaster.internal/ubuntu/ trusty/main libvorbis0a i386 1.3.2-1.3ubuntu1 [83.1 kB] Get:84 http://ftpmaster.internal/ubuntu/ trusty/main libvorbisenc2 i386 1.3.2-1.3ubuntu1 [66.9 kB] Get:85 http://ftpmaster.internal/ubuntu/ trusty/main libsndfile1 i386 1.0.25-7ubuntu2 [143 kB] Get:86 http://ftpmaster.internal/ubuntu/ trusty/main libwrap0 i386 7.6.q-25 [45.8 kB] Get:87 http://ftpmaster.internal/ubuntu/ trusty/main libpulse0 i386 1:4.0-0ubuntu7 [212 kB] Get:88 http://ftpmaster.internal/ubuntu/ trusty/main x11-common all 1:7.7+1ubuntu8 [49.8 kB] Get:89 http://ftpmaster.internal/ubuntu/ trusty/main libxtst6 i386 2:1.2.2-1 [13.8 kB] Get:90 http://ftpmaster.internal/ubuntu/ trusty/main libglapi-mesa i386 10.0.1-1ubuntu2 [21.2 kB] Get:91 http://ftpmaster.internal/ubuntu/ trusty/main libx11-xcb1 i386 2:1.6.2-1ubuntu2 [9396 B] Get:92 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-dri2-0 i386 1.10-2ubuntu1 [7150 B] Get:93 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-glx0 i386 1.10-2ubuntu1 [21.6 kB] Get:94 http://ftpmaster.internal/ubuntu/ trusty/main libxxf86vm1 i386 1:1.1.3-1 [11.8 kB] Get:95 http://ftpmaster.internal/ubuntu/ trusty/main libgl1-mesa-glx i386 10.0.1-1ubuntu2 [104 kB] Get:96 http://ftpmaster.internal/ubuntu/ trusty/main openjdk-7-jre i386 7u51-2.4.5-1ubuntu1 [178 kB] Get:97 http://ftpmaster.internal/ubuntu/ trusty/main default-jre i386 1:1.7-48ubuntu3 [938 B] Get:98 http://ftpmaster.internal/ubuntu/ trusty/main libatk-wrapper-java all 0.30.4-4 [30.2 kB] Get:99 http://ftpmaster.internal/ubuntu/ trusty/main libatk-wrapper-java-jni i386 0.30.4-4 [25.0 kB] Get:100 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 i386 0.6.8-2ubuntu1 [81.1 kB] Get:101 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 i386 0.9.3-5ubuntu3 [272 kB] Get:102 http://ftpmaster.internal/ubuntu/ trusty/main python3.3 i386 3.3.4~rc1-1ubuntu1 [133 kB] Get:103 http://ftpmaster.internal/ubuntu/ trusty-proposed/main python3-minimal i386 3.3.3-1 [23.4 kB] Get:104 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libpython3-stdlib i386 3.3.3-1 [7090 B] Get:105 http://ftpmaster.internal/ubuntu/ trusty-proposed/main python3 i386 3.3.3-1 [8682 B] Get:106 http://ftpmaster.internal/ubuntu/ trusty/main dh-python all 1.20131021-1ubuntu8 [50.2 kB] Get:107 http://ftpmaster.internal/ubuntu/ trusty/main file i386 1:5.14-2ubuntu1 [18.4 kB] Get:108 http://ftpmaster.internal/ubuntu/ trusty/main gettext-base i386 0.18.3.1-1ubuntu2 [47.9 kB] Get:109 http://ftpmaster.internal/ubuntu/ trusty/main libxml-commons-resolver1.1-java all 1.2-7build1 [91.6 kB] Get:110 http://ftpmaster.internal/ubuntu/ trusty/main libxml-commons-external-java all 1.4.01-2build1 [245 kB] Get:111 http://ftpmaster.internal/ubuntu/ trusty/main libxerces2-java all 2.11.0-7 [1362 kB] Get:112 http://ftpmaster.internal/ubuntu/ trusty/main ant all 1.9.3-1 [1869 kB] Get:113 http://ftpmaster.internal/ubuntu/ trusty/main ant-optional all 1.9.3-1 [301 kB] Get:114 http://ftpmaster.internal/ubuntu/ trusty/main dctrl-tools i386 2.23ubuntu1 [99.2 kB] Get:115 http://ftpmaster.internal/ubuntu/ trusty/main gettext i386 0.18.3.1-1ubuntu2 [815 kB] Get:116 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:117 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:118 http://ftpmaster.internal/ubuntu/ trusty/main apparmor-easyprof all 2.8.0-0ubuntu38 [20.1 kB] Get:119 http://ftpmaster.internal/ubuntu/ trusty/main dh-apparmor all 2.8.0-0ubuntu38 [7286 B] Get:120 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131127ubuntu2 [603 kB] Get:121 http://ftpmaster.internal/ubuntu/ trusty/main openjdk-7-jdk i386 7u51-2.4.5-1ubuntu1 [16.0 MB] Get:122 http://ftpmaster.internal/ubuntu/ trusty/main default-jdk i386 1:1.7-48ubuntu3 [930 B] Get:123 http://ftpmaster.internal/ubuntu/ trusty/main devscripts i386 2.14.1 [791 kB] Get:124 http://ftpmaster.internal/ubuntu/ trusty/main libarchive-zip-perl all 1.30-7 [90.1 kB] Get:125 http://ftpmaster.internal/ubuntu/ trusty/main javahelper all 0.45ubuntu1 [77.5 kB] Get:126 http://ftpmaster.internal/ubuntu/ trusty/main libhamcrest-java all 1.3-4 [385 kB] Get:127 http://ftpmaster.internal/ubuntu/ trusty/main junit4 all 4.11-2 [227 kB] Get:128 http://ftpmaster.internal/ubuntu/ trusty/main libapache-pom-java all 10-2build1 [4022 B] Get:129 http://ftpmaster.internal/ubuntu/ trusty/universe libatinject-jsr330-api-java all 1.0+ds1-1 [23.1 kB] Get:130 http://ftpmaster.internal/ubuntu/ trusty/main libcommons-lang-java all 2.6-3ubuntu2 [270 kB] Get:131 http://ftpmaster.internal/ubuntu/ trusty/main libcommons-cli-java all 1.2-3ubuntu1 [39.0 kB] Get:132 http://ftpmaster.internal/ubuntu/ trusty/main libcommons-codec-java all 1.9-1 [214 kB] Get:133 http://ftpmaster.internal/ubuntu/ trusty/universe libcommons-collections-java all 2.1.1-11 [160 kB] Get:134 http://ftpmaster.internal/ubuntu/ trusty/main libcommons-collections3-java all 3.2.1-6 [602 kB] Get:135 http://ftpmaster.internal/ubuntu/ trusty/main libcommons-pool-java all 1.6-2 [105 kB] Get:136 http://ftpmaster.internal/ubuntu/ trusty/main libcommons-dbcp-java all 1.4-3ubuntu1 [149 kB] Get:137 http://ftpmaster.internal/ubuntu/ trusty/main libcommons-parent-java all 22-2build1 [6968 B] Get:138 http://ftpmaster.internal/ubuntu/ trusty/main libcommons-logging-java all 1.1.3-1 [120 kB] Get:139 http://ftpmaster.internal/ubuntu/ trusty/universe libjsr305-java all 0.1~+svn49-4 [28.1 kB] Get:140 http://ftpmaster.internal/ubuntu/ trusty/universe libguava-java all 15.0-2ubuntu1 [1907 kB] Get:141 http://ftpmaster.internal/ubuntu/ trusty/main libservlet3.0-java all 7.0.50-1 [293 kB] Get:142 http://ftpmaster.internal/ubuntu/ trusty/universe libhsqldb-java all 2.2.9+dfsg-4ubuntu1 [1524 kB] Get:143 http://ftpmaster.internal/ubuntu/ trusty/universe libitext5-java all 5.4.5-1 [2003 kB] Get:144 http://ftpmaster.internal/ubuntu/ trusty/universe libjmol-java all 12.2.32+dfsg2-1 [8213 kB] Get:145 http://ftpmaster.internal/ubuntu/ trusty/main liblog4j1.2-java all 1.2.17-4ubuntu1 [387 kB] Get:146 http://ftpmaster.internal/ubuntu/ trusty/main icedtea-netx-common all 1.4.1-1ubuntu1 [846 kB] Get:147 http://ftpmaster.internal/ubuntu/ trusty/main icedtea-netx i386 1.4.1-1ubuntu1 [17.2 kB] Get:148 http://ftpmaster.internal/ubuntu/ trusty/universe libjson-simple-java all 1.1.1-1 [19.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 101 MB in 12s (7960 kB/s) Selecting previously unselected package libexpat1:i386. (Reading database ... 12003 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-4ubuntu1_i386.deb ... Unpacking libexpat1:i386 (2.1.0-4ubuntu1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu1_i386.deb ... Unpacking libmagic1:i386 (1:5.14-2ubuntu1) ... Selecting previously unselected package libssl1.0.0:i386. Preparing to unpack .../libssl1.0.0_1.0.1f-1ubuntu1_i386.deb ... Unpacking libssl1.0.0:i386 (1.0.1f-1ubuntu1) ... Selecting previously unselected package libpython3.3-minimal:i386. Preparing to unpack .../libpython3.3-minimal_3.3.4~rc1-1ubuntu1_i386.deb ... Unpacking libpython3.3-minimal:i386 (3.3.4~rc1-1ubuntu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.54ubuntu1_all.deb ... Unpacking mime-support (3.54ubuntu1) ... Selecting previously unselected package libmpdec2:i386. Preparing to unpack .../libmpdec2_2.4.0-6_i386.deb ... Unpacking libmpdec2:i386 (2.4.0-6) ... Selecting previously unselected package libpython3.3-stdlib:i386. Preparing to unpack .../libpython3.3-stdlib_3.3.4~rc1-1ubuntu1_i386.deb ... Unpacking libpython3.3-stdlib:i386 (3.3.4~rc1-1ubuntu1) ... Selecting previously unselected package python3.3-minimal. Preparing to unpack .../python3.3-minimal_3.3.4~rc1-1ubuntu1_i386.deb ... Unpacking python3.3-minimal (3.3.4~rc1-1ubuntu1) ... Selecting previously unselected package libasprintf0c2:i386. Preparing to unpack .../libasprintf0c2_0.18.3.1-1ubuntu2_i386.deb ... Unpacking libasprintf0c2:i386 (0.18.3.1-1ubuntu2) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../libglib2.0-0_2.39.3-0ubuntu4_i386.deb ... Unpacking libglib2.0-0:i386 (2.39.3-0ubuntu4) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../libpipeline1_1.2.6-1_i386.deb ... Unpacking libpipeline1:i386 (1.2.6-1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../libxau6_1%3a1.0.8-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.8-1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../libxdmcp6_1%3a1.1.1-1_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.1-1) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../libxcb1_1.10-2ubuntu1_i386.deb ... Unpacking libxcb1:i386 (1.10-2ubuntu1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../libx11-data_2%3a1.6.2-1ubuntu2_all.deb ... Unpacking libx11-data (2:1.6.2-1ubuntu2) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../libx11-6_2%3a1.6.2-1ubuntu2_i386.deb ... Unpacking libx11-6:i386 (2:1.6.2-1ubuntu2) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../libxext6_2%3a1.3.2-1_i386.deb ... Unpacking libxext6:i386 (2:1.3.2-1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../libxml2_2.9.1+dfsg1-3ubuntu3_i386.deb ... Unpacking libxml2:i386 (2.9.1+dfsg1-3ubuntu3) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-5_i386.deb ... Unpacking groff-base (1.22.2-5) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5ubuntu1_i386.deb ... Unpacking bsdmainutils (9.0.5ubuntu1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.6.6-1_i386.deb ... Unpacking man-db (2.6.6-1) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../libasound2-data_1.0.27.2-3ubuntu1_all.deb ... Unpacking libasound2-data (1.0.27.2-3ubuntu1) ... Selecting previously unselected package libasound2:i386. Preparing to unpack .../libasound2_1.0.27.2-3ubuntu1_i386.deb ... Unpacking libasound2:i386 (1.0.27.2-3ubuntu1) ... Selecting previously unselected package libasyncns0:i386. 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Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libmpdec2:i386 (2.4.0-6) ... Setting up libpython3.3-stdlib:i386 (3.3.4~rc1-1ubuntu1) ... Setting up python3.3-minimal (3.3.4~rc1-1ubuntu1) ... Setting up libasprintf0c2:i386 (0.18.3.1-1ubuntu2) ... Setting up libglib2.0-0:i386 (2.39.3-0ubuntu4) ... No schema files found: doing nothing. Setting up libpipeline1:i386 (1.2.6-1) ... Setting up libxau6:i386 (1:1.0.8-1) ... Setting up libxdmcp6:i386 (1:1.1.1-1) ... Setting up libxcb1:i386 (1.10-2ubuntu1) ... Setting up libx11-data (2:1.6.2-1ubuntu2) ... Setting up libx11-6:i386 (2:1.6.2-1ubuntu2) ... Setting up libxext6:i386 (2:1.3.2-1) ... Setting up libxml2:i386 (2.9.1+dfsg1-3ubuntu3) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.6-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libasound2-data (1.0.27.2-3ubuntu1) ... Setting up libasound2:i386 (1.0.27.2-3ubuntu1) ... Setting up libasyncns0:i386 (0.8-4ubuntu2) ... Setting up libatk1.0-data (2.10.0-2ubuntu1) ... Setting up libatk1.0-0:i386 (2.10.0-2ubuntu1) ... Setting up libgtk2.0-common (2.24.22-1ubuntu1) ... Setting up fonts-dejavu-core (2.34-1ubuntu1) ... Setting up ucf (3.0027+nmu1) ... Setting up fontconfig-config (2.11.0-0ubuntu4) ... Setting up libfreetype6:i386 (2.5.2-1ubuntu1) ... Setting up libfontconfig1:i386 (2.11.0-0ubuntu4) ... Setting up libpixman-1-0:i386 (0.30.2-2ubuntu1) ... Setting up libxcb-render0:i386 (1.10-2ubuntu1) ... Setting up libxcb-shm0:i386 (1.10-2ubuntu1) ... Setting up libxrender1:i386 (1:0.9.8-1) ... Setting up libcairo2:i386 (1.12.16-0ubuntu2) ... Setting up libavahi-common-data:i386 (0.6.31-4ubuntu1) ... Setting up libavahi-common3:i386 (0.6.31-4ubuntu1) ... Setting up libavahi-client3:i386 (0.6.31-4ubuntu1) ... Setting up libcups2:i386 (1.7.1-3) ... Setting up libjpeg-turbo8:i386 (1.3.0-0ubuntu2) ... Setting up libjpeg8:i386 (8c-2ubuntu8) ... Setting up libjasper1:i386 (1.900.1-14ubuntu3) ... Setting up libjbig0:i386 (2.0-2ubuntu4) ... Setting up libtiff5:i386 (4.0.3-7) ... Setting up libgdk-pixbuf2.0-common (2.30.3-0ubuntu1) ... Setting up libgdk-pixbuf2.0-0:i386 (2.30.3-0ubuntu1) ... Setting up libthai-data (0.1.20-3) ... Setting up libdatrie1:i386 (0.2.8-1) ... Setting up libthai0:i386 (0.1.20-3) ... Setting up fontconfig (2.11.0-0ubuntu4) ... Regenerating fonts cache... done. Setting up libpango-1.0-0:i386 (1.36.1-0ubuntu1) ... Setting up libgraphite2-3:i386 (1.2.4-1ubuntu1) ... Setting up libharfbuzz0b:i386 (0.9.25-1ubuntu1) ... Setting up libpangoft2-1.0-0:i386 (1.36.1-0ubuntu1) ... Setting up libpangocairo-1.0-0:i386 (1.36.1-0ubuntu1) ... Setting up libxcomposite1:i386 (1:0.4.4-1) ... Setting up libxfixes3:i386 (1:5.0.1-1ubuntu1) ... Setting up libxcursor1:i386 (1:1.1.14-1) ... Setting up libxdamage1:i386 (1:1.1.4-1ubuntu1) ... Setting up libxi6:i386 (2:1.7.1.901-1ubuntu1) ... Setting up libxinerama1:i386 (2:1.1.3-1) ... Setting up libxrandr2:i386 (2:1.4.2-1) ... Setting up shared-mime-info (1.2-0ubuntu1) ... Setting up libgtk2.0-0:i386 (2.24.22-1ubuntu1) ... Setting up openssl (1.0.1f-1ubuntu1) ... Setting up ca-certificates (20130906ubuntu1) ... Setting up libnspr4:i386 (2:4.10.2-1ubuntu1) ... Setting up tzdata-java (2013i-1) ... Setting up java-common (0.48ubuntu3) ... Setting up liblcms2-2:i386 (2.5-0ubuntu4) ... Setting up libpcsclite1:i386 (1.8.10-1ubuntu1) ... Setting up libgif4:i386 (4.1.6-11) ... Setting up libogg0:i386 (1.3.1-1ubuntu1) ... Setting up libflac8:i386 (1.3.0-2) ... Setting up libvorbis0a:i386 (1.3.2-1.3ubuntu1) ... Setting up libvorbisenc2:i386 (1.3.2-1.3ubuntu1) ... Setting up libsndfile1:i386 (1.0.25-7ubuntu2) ... Setting up libwrap0:i386 (7.6.q-25) ... Setting up libpulse0:i386 (1:4.0-0ubuntu7) ... Setting up x11-common (1:7.7+1ubuntu8) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libxtst6:i386 (2:1.2.2-1) ... Setting up libglapi-mesa:i386 (10.0.1-1ubuntu2) ... Setting up libx11-xcb1:i386 (2:1.6.2-1ubuntu2) ... Setting up libxcb-dri2-0:i386 (1.10-2ubuntu1) ... Setting up libxcb-glx0:i386 (1.10-2ubuntu1) ... Setting up libxxf86vm1:i386 (1:1.1.3-1) ... Setting up libgl1-mesa-glx:i386 (10.0.1-1ubuntu2) ... update-alternatives: using /usr/lib/i386-linux-gnu/mesa/ld.so.conf to provide /etc/ld.so.conf.d/i386-linux-gnu_GL.conf (i386-linux-gnu_gl_conf) in auto mode Setting up libcroco3:i386 (0.6.8-2ubuntu1) ... Setting up libunistring0:i386 (0.9.3-5ubuntu3) ... Setting up python3.3 (3.3.4~rc1-1ubuntu1) ... Setting up python3-minimal (3.3.3-1) ... Setting up libpython3-stdlib:i386 (3.3.3-1) ... Setting up file (1:5.14-2ubuntu1) ... Setting up gettext-base (0.18.3.1-1ubuntu2) ... Setting up libxml-commons-resolver1.1-java (1.2-7build1) ... Setting up libxml-commons-external-java (1.4.01-2build1) ... Setting up libxerces2-java (2.11.0-7) ... Setting up dctrl-tools (2.23ubuntu1) ... Setting up gettext (0.18.3.1-1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up libarchive-zip-perl (1.30-7) ... Setting up libhamcrest-java (1.3-4) ... Setting up libapache-pom-java (10-2build1) ... Setting up libatinject-jsr330-api-java (1.0+ds1-1) ... Setting up libcommons-lang-java (2.6-3ubuntu2) ... Setting up libcommons-cli-java (1.2-3ubuntu1) ... Setting up libcommons-codec-java (1.9-1) ... Setting up libcommons-collections-java (2.1.1-11) ... Setting up libcommons-collections3-java (3.2.1-6) ... Setting up libcommons-pool-java (1.6-2) ... Setting up libcommons-dbcp-java (1.4-3ubuntu1) ... Setting up libcommons-parent-java (22-2build1) ... Setting up libcommons-logging-java (1.1.3-1) ... Setting up libjsr305-java (0.1~+svn49-4) ... Setting up libguava-java (15.0-2ubuntu1) ... Setting up libservlet3.0-java (7.0.50-1) ... Setting up libhsqldb-java (2.2.9+dfsg-4ubuntu1) ... Setting up libitext5-java (5.4.5-1) ... Setting up libjmol-java (12.2.32+dfsg2-1) ... Setting up liblog4j1.2-java (1.2.17-4ubuntu1) ... Setting up icedtea-netx-common (1.4.1-1ubuntu1) ... Setting up libjson-simple-java (1.1.1-1) ... Setting up python3 (3.3.3-1) ... running python rtupdate hooks for python3.3... running python post-rtupdate hooks for python3.3... Setting up dh-python (1.20131021-1ubuntu8) ... Setting up apparmor-easyprof (2.8.0-0ubuntu38) ... Setting up dh-apparmor (2.8.0-0ubuntu38) ... Setting up debhelper (9.20131127ubuntu2) ... Setting up devscripts (2.14.1) ... Setting up javahelper (0.45ubuntu1) ... Setting up libnss3-nssdb (2:3.15.4-1ubuntu5) ... Setting up libnss3:i386 (2:3.15.4-1ubuntu5) ... Setting up libnss3-1d:i386 (2:3.15.4-1ubuntu5) ... Setting up openjdk-7-jre-headless:i386 (7u51-2.4.5-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up default-jre-headless (1:1.7-48ubuntu3) ... Setting up libatk-wrapper-java (0.30.4-4) ... Setting up libatk-wrapper-java-jni:i386 (0.30.4-4) ... Setting up openjdk-7-jre:i386 (7u51-2.4.5-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up default-jre (1:1.7-48ubuntu3) ... Setting up ant (1.9.3-1) ... Setting up ant-optional (1.9.3-1) ... Setting up openjdk-7-jdk:i386 (7u51-2.4.5-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/javah to provide /usr/bin/javah (javah) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode Setting up default-jdk (1:1.7-48ubuntu3) ... Setting up junit4 (4.11-2) ... Setting up icedtea-netx:i386 (1.4.1-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/javaws to provide /usr/bin/javaws (javaws) in auto mode update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/itweb-settings to provide /usr/bin/itweb-settings (itweb-settings) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/javaws to provide /usr/bin/javaws (javaws) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-i386/jre/bin/itweb-settings to provide /usr/bin/itweb-settings (itweb-settings) in auto mode Setting up ca-certificates-java (20130815) ... done. Processing triggers for libc-bin (2.18-0ubuntu6) ... Processing triggers for ca-certificates (20130906ubuntu1) ... Updating certificates in /etc/ssl/certs... 166 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d.... Adding debian:cacert.org_class3.pem Adding debian:cacert.org_root.pem Adding debian:A-Trust-nQual-03.pem Adding debian:ACEDICOM_Root.pem Adding debian:AC_Raíz_Certicámara_S.A..pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AddTrust_External_Root.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:America_Online_Root_Certification_Authority_1.pem Adding debian:America_Online_Root_Certification_Authority_2.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_CA_1.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig.pem Adding debian:CA_Disig_Root_R1.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CNNIC_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:Certigna.pem Adding debian:Certinomis_-_Autorité_Racine.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Certum_Root_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem Adding debian:ComSign_CA.pem Adding debian:ComSign_Secured_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_1.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_3.pem Adding debian:E-Guven_Kok_Elektronik_Sertifika_Hizmet_Saglayicisi.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem Adding debian:EC-ACC.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust.net_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Equifax_Secure_CA.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:Firmaprofesional_Root_CA.pem Adding debian:GTE_CyberTrust_Global_Root.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:IGC_A.pem Adding debian:Izenpe.com.pem Adding debian:Juur-SK.pem Adding debian:Microsec_e-Szigno_Root_CA.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:PSCProcert.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:RSA_Root_Certificate_1.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:StartCom_Certification_Authority_2.pem Adding debian:StartCom_Certification_Authority_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:Swisscom_Root_CA_2.pem Adding debian:Swisscom_Root_EV_CA_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TC_TrustCenter_Class_2_CA_II.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:TC_TrustCenter_Universal_CA_I.pem Adding debian:TDC_Internet_Root_CA.pem Adding debian:TDC_OCES_Root_CA.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_1.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Taiwan_GRCA.pem Adding debian:Thawte_Premium_Server_CA.pem Adding debian:Thawte_Server_CA.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem Adding debian:UTN_DATACorp_SGC_Root_CA.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:ValiCert_Class_1_VA.pem Adding debian:ValiCert_Class_2_VA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:Wells_Fargo_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:spi-cacert-2008.pem done. done. Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.18-0ubuntu6 make_3.81-8.2ubuntu3 dpkg-dev_1.17.5ubuntu2 gcc-4.8_4.8.2-14ubuntu4 g++-4.8_4.8.2-14ubuntu4 binutils_2.24-2ubuntu3 libstdc++-4.8-dev_4.8.2-14ubuntu4 libstdc++6_4.8.2-14ubuntu4 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Mon Feb 3 09:41:32 2014 UTC using RSA key ID 326D8438 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./biojava3-live_3.0.7+dfsg-1.dsc dpkg-source: info: extracting biojava3-live in biojava3-live-3.0.7+dfsg dpkg-source: info: unpacking biojava3-live_3.0.7+dfsg.orig.tar.bz2 dpkg-source: info: unpacking biojava3-live_3.0.7+dfsg-1.debian.tar.xz dpkg-source: info: applying use_simple_json dpkg-source: info: applying fix_ascii_characters_mapping dpkg-source: info: applying skip_network_related_tests dpkg-source: info: applying fix_itext_class_updates dpkg-source: info: applying fix_uselog4j1 dpkg-buildpackage: source package biojava3-live dpkg-buildpackage: source version 3.0.7+dfsg-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build biojava3-live-3.0.7+dfsg dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh clean --with javahelper dh_testdir dh_auto_clean jh_clean debian/rules override_dh_clean make[1]: Entering directory `/build/buildd/biojava3-live-3.0.7+dfsg' dh_clean rm -rf build rm -rf dist rm -rf javadoc rm -rf test rm -f biojava3-*/build.xml rm -rf biojavadoc rm -rf doc make[1]: Leaving directory `/build/buildd/biojava3-live-3.0.7+dfsg' debian/rules build dh build --with javahelper dh_testdir debian/rules override_dh_auto_configure make[1]: Entering directory `/build/buildd/biojava3-live-3.0.7+dfsg' dh_auto_configure sed -e 's/BJLIB/biojava3-forester/g' debian/build.xml > biojava3-forester/build.xml sed -e 's/BJLIB/biojava3-aa-prop/g' debian/build.xml > biojava3-aa-prop/build.xml sed -e 's/BJLIB/biojava3-core/g' debian/build.xml > biojava3-core/build.xml sed -e 's/BJLIB/biojava3-alignment/g' debian/build.xml > biojava3-alignment/build.xml sed -e 's/BJLIB/biojava3-genome/g' debian/build.xml > biojava3-genome/build.xml sed -e 's/BJLIB/biojava3-modfinder/g' debian/build.xml > biojava3-modfinder/build.xml sed -e 's/BJLIB/biojava3-phylo/g' debian/build.xml > biojava3-phylo/build.xml sed -e 's/BJLIB/biojava3-sequencing/g' debian/build.xml > biojava3-sequencing/build.xml sed -e 's/BJLIB/biojava3-protein-disorder/g' debian/build.xml > biojava3-protein-disorder/build.xml sed -e 's/BJLIB/biojava3-structure/g' debian/build.xml > biojava3-structure/build.xml sed -e 's/BJLIB/biojava3-ws/g' debian/build.xml > biojava3-ws/build.xml sed -e 's/BJLIB/biojava3-structure-gui/g' debian/build.xml > biojava3-structure-gui/build.xml make[1]: Leaving directory `/build/buildd/biojava3-live-3.0.7+dfsg' jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/biojava3-live-3.0.7+dfsg' cd biojava3-forester && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-forester/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-forester/classes [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/dist [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-forester/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 332 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-forester/classes [javac] Note: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java uses or overrides 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] Warning: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-forester/src/main/resources does not exist. jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-forester.jar BUILD SUCCESSFUL Total time: 6 seconds cd biojava3-core && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-core/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-core/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-core/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 134 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-core/classes [javac] Note: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-core/src/main/java/org/biojava3/core/sequence/ProteinSequence.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 1 file to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-core/classes jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-core.jar BUILD SUCCESSFUL Total time: 3 seconds cd biojava3-phylo && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-phylo/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-phylo/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-phylo/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 10 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-phylo/classes [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 1 file to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-phylo/classes jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-phylo.jar BUILD SUCCESSFUL Total time: 1 second cd biojava3-alignment && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-alignment/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-alignment/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-alignment/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 65 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-alignment/classes [copy] Copying 20 files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-alignment/classes jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-alignment.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava3-aa-prop && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-aa-prop/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-aa-prop/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 31 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes [javac] Creating empty /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/xml/package-info.class [javac] Creating empty /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/profeat/convertor/package-info.class [javac] Creating empty /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/package-info.class [javac] Creating empty /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/profeat/package-info.class [copy] Copying 10 files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-aa-prop.jar BUILD SUCCESSFUL Total time: 1 second cd biojava3-genome && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-genome/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-genome/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-genome/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 20 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-genome/classes [javac] Note: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Writer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Warning: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-genome/src/main/resources does not exist. jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-genome.jar BUILD SUCCESSFUL Total time: 1 second cd biojava3-sequencing && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-sequencing/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-sequencing/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-sequencing/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 19 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-sequencing/classes [javac] Note: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqTools.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] Creating empty /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-sequencing/classes/org/biojava3/sequencing/io/fastq/package-info.class [copy] Warning: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-sequencing/src/main/resources does not exist. jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-sequencing.jar BUILD SUCCESSFUL Total time: 1 second cd biojava3-structure && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-structure/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-structure/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-structure/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 314 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-structure/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 63 files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-structure/classes jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-structure.jar BUILD SUCCESSFUL Total time: 5 seconds cd biojava3-structure-gui && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-structure-gui/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-structure-gui/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-structure-gui/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 105 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-structure-gui/classes [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 14 files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-structure-gui/classes jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-structure-gui.jar BUILD SUCCESSFUL Total time: 3 seconds cd biojava3-modfinder && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-modfinder/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-modfinder/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-modfinder/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 21 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-modfinder/classes [copy] Copying 1 file to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-modfinder/classes jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-modfinder.jar BUILD SUCCESSFUL Total time: 1 second cd biojava3-protein-disorder && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-protein-disorder/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-protein-disorder/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 13 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes [javac] Creating empty /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes/org/biojava3/data/sequence/package-info.class [javac] Creating empty /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes/org/biojava3/ronn/package-info.class [copy] Copying 10 files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-protein-disorder.jar BUILD SUCCESSFUL Total time: 1 second cd biojava3-ws && ant jar Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-ws/build.xml compile: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-ws/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-ws/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 20 source files to /build/buildd/biojava3-live-3.0.7+dfsg/build/biojava3-ws/classes [copy] Warning: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/resources does not exist. jar: [jar] Building jar: /build/buildd/biojava3-live-3.0.7+dfsg/dist/biojava3-ws.jar BUILD SUCCESSFUL Total time: 1 second # make doc rm -rf biojavadoc mkdir biojavadoc cp -r biojava3-*/src biojavadoc/ sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml cd biojavadoc && ant javadocs Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/build.xml javadocs: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/javadoc [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/doc/biojava [javadoc] Generating Javadoc [javadoc] Javadoc execution [javadoc] Loading source files for package org.biojava.bio.structure... [javadoc] Loading source files for package org.biojava.bio.structure.align... [javadoc] Loading source files for package org.biojava.bio.structure.align.ce... [javadoc] Loading source files for package org.biojava.bio.structure.align.client... [javadoc] Loading source files for package org.biojava.bio.structure.align.events... [javadoc] Loading source files for package org.biojava.bio.structure.align.fatcat... [javadoc] Loading source files for package org.biojava.bio.structure.align.fatcat.calc... [javadoc] Loading source files for package org.biojava.bio.structure.align.gui... [javadoc] Loading source files for package org.biojava.bio.structure.align.gui.aligpanel... [javadoc] Loading source files for package org.biojava.bio.structure.align.gui.autosuggest... [javadoc] Loading source files for package org.biojava.bio.structure.align.gui.jmol... [javadoc] Loading source files for package org.biojava.bio.structure.align.helper... [javadoc] Loading source files for package org.biojava.bio.structure.align.model... [javadoc] Loading source files for package org.biojava.bio.structure.align.pairwise... [javadoc] Loading source files for package org.biojava.bio.structure.align.seq... [javadoc] Loading source files for package org.biojava.bio.structure.align.util... [javadoc] Loading source files for package org.biojava.bio.structure.align.webstart... [javadoc] Loading source files for package org.biojava.bio.structure.align.xml... [javadoc] Loading source files for package org.biojava.bio.structure.cath... [javadoc] Loading source files for package org.biojava.bio.structure.domain... [javadoc] Loading source files for package org.biojava.bio.structure.domain.pdp... [javadoc] Loading source files for package org.biojava.bio.structure.gui... [javadoc] Loading source files for package org.biojava.bio.structure.gui.events... [javadoc] Loading source files for package org.biojava.bio.structure.gui.util... [javadoc] Loading source files for package org.biojava.bio.structure.gui.util.color... [javadoc] Loading source files for package org.biojava.bio.structure.io... [javadoc] Loading source files for package org.biojava.bio.structure.io.mmcif... [javadoc] Loading source files for package org.biojava.bio.structure.io.mmcif.chem... [javadoc] Loading source files for package org.biojava.bio.structure.io.mmcif.model... [javadoc] Loading source files for package org.biojava.bio.structure.io.sifts... [javadoc] Loading source files for package org.biojava.bio.structure.io.util... [javadoc] Loading source files for package org.biojava.bio.structure.jama... [javadoc] Loading source files for package org.biojava.bio.structure.math... [javadoc] Loading source files for package org.biojava.bio.structure.quaternary... [javadoc] Loading source files for package org.biojava.bio.structure.quaternary.io... [javadoc] Loading source files for package org.biojava.bio.structure.rcsb... 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[javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/StructureAlignmentJmol.java:80: error: package org.jmol.api does not exist [javadoc] import org.jmol.api.JmolViewer; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:56: error: package org.jmol.adapter.smarter does not exist [javadoc] import org.jmol.adapter.smarter.SmarterJmolAdapter; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:57: error: package org.jmol.api does not exist [javadoc] import org.jmol.api.JmolAdapter; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:59: error: package org.jmol.api does not exist [javadoc] import org.jmol.api.JmolStatusListener; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:60: error: package org.jmol.api does not exist [javadoc] import org.jmol.api.JmolViewer; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:69: error: cannot find symbol [javadoc] private JmolViewer viewer; [javadoc] ^ [javadoc] symbol: class JmolViewer [javadoc] location: class JmolPanel [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:70: error: cannot find symbol [javadoc] private JmolAdapter adapter; [javadoc] ^ [javadoc] symbol: class JmolAdapter [javadoc] location: class JmolPanel [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:71: error: cannot find symbol [javadoc] JmolStatusListener statusListener; [javadoc] ^ [javadoc] symbol: class JmolStatusListener [javadoc] location: class JmolPanel [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:105: error: cannot find symbol [javadoc] public JmolViewer getViewer() { [javadoc] ^ [javadoc] symbol: class JmolViewer [javadoc] location: class JmolPanel [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:109: error: cannot find symbol [javadoc] public JmolAdapter getAdapter(){ [javadoc] ^ [javadoc] symbol: class JmolAdapter [javadoc] location: class JmolPanel [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:113: error: cannot find symbol [javadoc] public JmolStatusListener getStatusListener(){ [javadoc] ^ [javadoc] symbol: class JmolStatusListener [javadoc] location: class JmolPanel [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:32: error: package org.jmol.api does not exist [javadoc] import org.jmol.api.JmolStatusListener; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:33: error: package org.jmol.constant does not exist [javadoc] import org.jmol.constant.EnumCallback; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:35: error: cannot find symbol [javadoc] public class MyJmolStatusListener implements JmolStatusListener { [javadoc] ^ [javadoc] symbol: class JmolStatusListener [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:112: error: cannot find symbol [javadoc] public void notifyCallback(EnumCallback arg0, Object[] arg1) { [javadoc] ^ [javadoc] symbol: class EnumCallback [javadoc] location: class MyJmolStatusListener [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:118: error: cannot find symbol [javadoc] public boolean notifyEnabled(EnumCallback arg0) { [javadoc] ^ [javadoc] symbol: class EnumCallback [javadoc] location: class MyJmolStatusListener [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:33: error: package javax.jnlp does not exist [javadoc] import javax.jnlp.BasicService; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:34: error: package javax.jnlp does not exist [javadoc] import javax.jnlp.FileContents; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:35: error: package javax.jnlp does not exist [javadoc] import javax.jnlp.PersistenceService; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:36: error: package javax.jnlp does not exist [javadoc] import javax.jnlp.ServiceManager; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:37: error: package javax.jnlp does not exist [javadoc] import javax.jnlp.UnavailableServiceException; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:56: error: cannot find symbol [javadoc] PersistenceService ps; [javadoc] ^ [javadoc] symbol: class PersistenceService [javadoc] location: class PersistentConfig [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:57: error: cannot find symbol [javadoc] BasicService bs ; [javadoc] ^ [javadoc] symbol: class BasicService [javadoc] location: class PersistentConfig [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:60: error: cannot find symbol [javadoc] throws UnavailableServiceException [javadoc] ^ [javadoc] symbol: class UnavailableServiceException [javadoc] location: class PersistentConfig [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java:34: error: package org.apache.log4j does not exist [javadoc] import org.apache.log4j.LogManager; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java:35: error: package org.apache.log4j does not exist [javadoc] import org.apache.log4j.Logger; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java:47: error: cannot find symbol [javadoc] private static final Logger logger = LogManager.getLogger(ReadUtils.class.getPackage().getName()); [javadoc] ^ [javadoc] symbol: class Logger [javadoc] location: class ReadUtils [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java:28: error: package org.apache.log4j does not exist [javadoc] import org.apache.log4j.LogManager; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java:29: error: package org.apache.log4j does not exist [javadoc] import org.apache.log4j.Logger; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java:61: error: cannot find symbol [javadoc] private static final Logger logger = LogManager.getLogger(RCSBLigandsFactory.class.getPackage().getName()); [javadoc] ^ [javadoc] symbol: class Logger [javadoc] location: class RCSBLigandsFactory [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java:26: error: package org.apache.log4j does not exist [javadoc] import org.apache.log4j.LogManager; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java:27: error: package org.apache.log4j does not exist [javadoc] import org.apache.log4j.Logger; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java:57: error: cannot find symbol [javadoc] private static final Logger logger = LogManager.getLogger(RCSBDescriptionFactory.class.getPackage().getName()); [javadoc] ^ [javadoc] symbol: class Logger [javadoc] location: class RCSBDescriptionFactory [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/scop/Astral.java:31: error: package org.apache.log4j does not exist [javadoc] import org.apache.log4j.LogManager; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/scop/Astral.java:32: error: package org.apache.log4j does not exist [javadoc] import org.apache.log4j.Logger; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/scop/Astral.java:102: error: cannot find symbol [javadoc] private static final Logger logger = LogManager.getLogger(Astral.class.getName()); [javadoc] ^ [javadoc] symbol: class Logger [javadoc] location: class Astral [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java:26: error: package com.google.common.io does not exist [javadoc] import com.google.common.io.CharStreams; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java:27: error: package com.google.common.io does not exist [javadoc] import com.google.common.io.InputSupplier; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java:28: error: package com.google.common.io does not exist [javadoc] import com.google.common.io.LineProcessor; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java:45: error: cannot find symbol [javadoc] static void parse(final InputSupplier supplier, final ParseListener listener) [javadoc] ^ [javadoc] symbol: class InputSupplier [javadoc] location: class FastqParser [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java:68: error: cannot find symbol [javadoc] private static class FastqParserLineProcessor implements LineProcessor [javadoc] ^ [javadoc] symbol: class LineProcessor [javadoc] location: class FastqParser [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/StreamingFastqParser.java:26: error: package com.google.common.io does not exist [javadoc] import com.google.common.io.InputSupplier; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/StreamingFastqParser.java:44: error: cannot find symbol [javadoc] static void stream(final InputSupplier supplier, [javadoc] ^ [javadoc] symbol: class InputSupplier [javadoc] location: class StreamingFastqParser [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:35: error: package com.google.common.collect does not exist [javadoc] import com.google.common.collect.Iterables; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:36: error: package com.google.common.collect does not exist [javadoc] import com.google.common.collect.Lists; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:38: error: package com.google.common.io does not exist [javadoc] import com.google.common.io.InputSupplier; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:39: error: package com.google.common.io does not exist [javadoc] import com.google.common.io.Files; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:40: error: package com.google.common.io does not exist [javadoc] import com.google.common.io.Resources; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqReader.java:30: error: package com.google.common.io does not exist [javadoc] import com.google.common.io.InputSupplier; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:59: error: cannot find symbol [javadoc] public final void parse(final InputSupplier supplier, [javadoc] ^ [javadoc] symbol: class InputSupplier [javadoc] location: class AbstractFastqReader [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:67: error: cannot find symbol [javadoc] public final void stream(final InputSupplier supplier, [javadoc] ^ [javadoc] symbol: class InputSupplier [javadoc] location: class AbstractFastqReader [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqReader.java:47: error: cannot find symbol [javadoc] void parse(InputSupplier supplier, ParseListener listener) throws IOException; [javadoc] ^ [javadoc] symbol: class InputSupplier [javadoc] location: interface FastqReader [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqReader.java:56: error: cannot find symbol [javadoc] void stream(InputSupplier supplier, StreamListener listener) throws IOException; [javadoc] ^ [javadoc] symbol: class InputSupplier [javadoc] location: interface FastqReader [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqTools.java:25: error: package com.google.common.collect does not exist [javadoc] import com.google.common.collect.Lists; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqTools.java:26: error: package com.google.common.collect does not exist [javadoc] import com.google.common.collect.ImmutableList; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:16: error: package org.json.simple does not exist [javadoc] import org.json.simple.JSONArray; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:17: error: package org.json.simple does not exist [javadoc] import org.json.simple.JSONObject; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:18: error: package org.json.simple does not exist [javadoc] import org.json.simple.JSONValue; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:29: error: package org.apache.commons.codec.binary does not exist [javadoc] import org.apache.commons.codec.binary.Base64; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:38: error: package com.itextpdf.text does not exist [javadoc] import com.itextpdf.text.Document; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:39: error: package com.itextpdf.text does not exist [javadoc] import com.itextpdf.text.DocumentException; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:40: error: package com.itextpdf.text does not exist [javadoc] import com.itextpdf.text.FontFactory; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:41: error: package com.itextpdf.text does not exist [javadoc] import com.itextpdf.text.Rectangle; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:42: error: package com.itextpdf.awt does not exist [javadoc] import com.itextpdf.awt.DefaultFontMapper; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:43: error: package com.itextpdf.text.pdf does not exist [javadoc] import com.itextpdf.text.pdf.PdfContentByte; [javadoc] ^ [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:44: error: package com.itextpdf.text.pdf does not exist [javadoc] import com.itextpdf.text.pdf.PdfWriter; [javadoc] ^ [javadoc] Standard Doclet version 1.7.0_51 [javadoc] Building tree for all the packages and classes... [javadoc] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.6.0/docs/api/package-list [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java:55: warning - Tag @see: missing final '>': "RCSB RESTful [javadoc] [javadoc] TODO: Handle queries with more than 1 PDB Id." [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @see:illegal character: "123" in "{@link GroupType#WATERNAMES}" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @see:illegal character: "64" in "{@link GroupType#WATERNAMES}" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:140: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:152: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:170: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:181: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:192: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:213: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:263: warning - @param argument "chainId" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:271: warning - @param argument "chainId" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Calc.java:146: warning - Tag @link: reference not found: subtract [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Calc.java:146: warning - Tag @link: reference not found: subtract [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/DBRef.java:199: warning - Tag @see: can't find setChainId(Character) in org.biojava.bio.structure.DBRef [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Element.java:392: warning - Tag @link: reference not found: T [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @see: reference not found: {@link GroupType#WATERNAMES} [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @link: can't find WATERNAMES in org.biojava.bio.structure.GroupType [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @see: reference not found: {@link GroupType#WATERNAMES} [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/PDBStatus.java:69: warning - Tag @link: can't find getReplacement(String, boolean) in org.biojava.bio.structure.PDBStatus [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/PDBStatus.java:223: warning - Tag @link: can't find getReplacement(String,boolean) in org.biojava.bio.structure.PDBStatus [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/PDBStatus.java:108: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/PDBStatus.java:108: warning - @param argument "statusStrUpper" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Structure.java:606: warning - @param argument "PDBCrystallographicInfo" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/StructureImpl.java:741: warning - @param argument "PDBCrystallographicInfo" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/StructureTools.java:1213: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/SVDSuperimposer.java:336: warning - Tag @see:illegal character: "123" in "{@link #getTMScore(Atom[], Atom[], int, int)}, which normalizes by the minimum length" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/SVDSuperimposer.java:336: warning - Tag @see:illegal character: "64" in "{@link #getTMScore(Atom[], Atom[], int, int)}, which normalizes by the minimum length" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/SVDSuperimposer.java:336: warning - Tag @see: reference not found: {@link #getTMScore(Atom[], Atom[], int, int)}, which normalizes by the minimum length [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/AbstractUserArgumentProcessor.java:665: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/CECalculator.java:363: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/CeCalculatorEnhanced.java:366: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/CeParameters.java:346: warning - @param argument "maxNrIterationsForOptimization" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/OptimalCECPMain.java:191: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/OptimalCECPMain.java:471: warning - Tag @link: can't find alignHeuristic(Atom[], Atom[], Object) in org.biojava.bio.structure.align.ce.OptimalCECPMain [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/StartupParameters.java:67: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/StartupParameters.java:79: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/fatcat/calc/AFPCalculator.java:155: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/fatcat/calc/AFPCalculator.java:179: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/fatcat/calc/AFPChainer.java:384: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/fatcat/calc/AFPChainer.java:408: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/fatcat/calc/AFPChainer.java:668: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/fatcat/calc/AFPChainer.java:703: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/DisplayAFP.java:143: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/DotPlotPanel.java:67: warning - @param argument "background" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1051: warning - Tag @see: malformed: "#getOptLength(), the number of aligned residues in the final alignment." [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1372: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1051: warning - Tag @see: reference not found: #getOptLength(), the number of aligned residues in the final alignment. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/model/AfpChainWriter.java:129: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AFPAlignmentDisplay.java:442: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:254: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:448: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:586: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:738: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:777: warning - Tag @see:illegal character: "123" in "{@link CECalculator#calc_rmsd(Atom[], Atom[], int, boolean, boolean)} [javadoc] contains much of the same code, but stores results in a CECalculator [javadoc] instance rather than an AFPChain" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:777: warning - Tag @see:illegal character: "64" in "{@link CECalculator#calc_rmsd(Atom[], Atom[], int, boolean, boolean)} [javadoc] contains much of the same code, but stores results in a CECalculator [javadoc] instance rather than an AFPChain" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:883: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:412: warning - @param argument "afpChain" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:738: warning - @param argument "optLength" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:777: warning - Tag @see: reference not found: {@link CECalculator#calc_rmsd(Atom[], Atom[], int, boolean, boolean)} [javadoc] contains much of the same code, but stores results in a CECalculator [javadoc] instance rather than an AFPChain [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:486: warning - @param argument "" is not a type parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:301: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:1069: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:258: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:715: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:794: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:794: warning - @param argument "fetchCurrent" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/CacheFactory.java:12: warning - @Deprecated is an unknown tag -- same as a known tag except for case. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/RotationAxis.java:75: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/RotationAxis.java:86: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/util/RotationAxis.java:254: warning - Tag @link: can't find evalString() in org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:48: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:508: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:48: warning - Parameter "name1" is documented more than once. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/cath/CathDatabase.java:109: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/cath/CathDatabase.java:116: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/domain/RemotePDPProvider.java:217: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/ContinuousColorMapperTransform.java:65: warning - @param argument "the" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/DefaultMatrixMapper.java:49: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:88: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:145: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:186: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:194: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:201: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:223: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:233: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:254: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:271: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:108: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:120: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:86: warning - @param argument "type" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:86: warning - @param argument "numcomponents" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/gui/util/color/LinearColorInterpolator.java:147: warning - @param argument "interpDirection" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:248: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:66: warning - Tag @link: reference not found: FastaSequence FastaSequences [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:87: warning - Tag @link: reference not found: cpSite [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:110: warning - Tag @link: reference not found: cpSite [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:87: warning - Tag @link: reference not found: cpSite [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:110: warning - Tag @link: reference not found: cpSite [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FileConvert.java:320: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FileConvert.java:335: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FileConvert.java:357: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:46: warning - @link# is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:46: warning - @link# is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:262: warning - @returns is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:288: warning - @param argument "accepted" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureProvider.java:20: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureProvider.java:27: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java:3203: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:448: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:373: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:384: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:518: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:973: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:986: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:986: warning - @param argument "fetchCurrent" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/SandboxStyleStructureProvider.java:92: warning - @ is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/SeqRes2AtomAligner.java:243: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/SeqRes2AtomAligner.java:243: warning - @param argument "seqRes" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/SeqRes2AtomAligner.java:243: warning - @param argument "atomList" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:69: warning - Tag @see:illegal character: "123" in "{@link #matchSequenceToStructure(ProteinSequence, Structure)}" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:69: warning - Tag @see:illegal character: "64" in "{@link #matchSequenceToStructure(ProteinSequence, Structure)}" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:115: warning - Tag @see:illegal character: "123" in "{@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [javadoc] does the heavy lifting." [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:115: warning - Tag @see:illegal character: "64" in "{@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [javadoc] does the heavy lifting." [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:232: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:69: warning - Tag @see: reference not found: {@link #matchSequenceToStructure(ProteinSequence, Structure)} [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:115: warning - Tag @see: reference not found: {@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [javadoc] does the heavy lifting. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/mmcif/DownloadChemCompProvider.java:435: warning - @param argument "flag" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.java:268: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.java:401: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/sifts/SiftsXMLParser.java:142: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/util/FileDownloadUtils.java:232: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/math/SparseSquareMatrix.java:99: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/math/SparseSquareMatrix.java:133: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/math/SparseVector.java:97: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/math/SparseVector.java:118: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/math/SparseVector.java:128: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/math/SparseVector.java:140: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/BioAssemblyTools.java:321: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/BioAssemblyTools.java:263: warning - @param argument "structure" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/BiologicalAssemblyBuilder.java:155: warning - @param argument "assemblyId" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/ModelTransformationMatrix.java:51: warning - Tag @see: reference not found: org.rcsb.mbt.glscene.jogl.GLTransformationMatrix [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/ModelTransformationMatrix.java:51: warning - Tag @see: reference not found: org.rcsb.vf.glscene.jogl.GLTransformationList [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/ModelTransformationMatrix.java:51: warning - Tag @see: reference not found: org.rcsb.mbt.model.geometry.ModelTransformationList [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/io/BioUnitDataProvider.java:48: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/io/MmCifPDBBiolAssemblyProvider.java:153: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/io/RawBioUnitDataProvider.java:29: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/io/RawBioUnitDataProvider.java:35: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/io/RawBioUnitDataProvider.java:41: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/io/RawBioUnitDataProvider.java:48: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/io/RawBioUnitDataProvider.java:62: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/quaternary/io/RawBioUnitDataProvider.java:70: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/scop/Astral.java:122: warning - @param argument "An" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/scop/ScopInstallation.java:668: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/scop/ScopDescription.java:144: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/scop/ScopDescription.java:166: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/scop/ScopFactory.java:102: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/server/PrepareIndexFile.java:161: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convertor.java:21: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convertor.java:21: warning - Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/alignment/io/StockholmFileAnnotation.java:312: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/alignment/io/StockholmFileAnnotation.java:324: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/alignment/io/StockholmFileAnnotation.java:337: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/alignment/io/StockholmFileAnnotation.java:171: warning - @param argument "dbReference" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/alignment/io/StockholmFileParser.java:348: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/alignment/io/StockholmStructure.java:199: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/alignment/io/StockholmStructure.java:210: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:171: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:311: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:331: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:348: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:404: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:520: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:529: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:538: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:564: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:574: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:582: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:591: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:600: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link: reference not found: http://www.sequenceontology.org/gff3.shtml [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "58" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "126" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link: reference not found: http://www.sequenceontology.org/gff3.shtml [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link: reference not found: http://biowiki.org/~yam/bioe131/GFF.ppt [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:105: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:114: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:132: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:144: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:132: warning - @param argument "begin" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:132: warning - @param argument "end" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/GeneSequence.java:63: warning - @param argument "parentDNASequence" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/RNASequence.java:85: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/RNASequence.java:95: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/RNASequence.java:103: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/RNASequence.java:111: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/RNASequence.java:122: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:77: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:92: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:104: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:134: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:190: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:204: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:213: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:231: warning - @param argument "startCodonSequence" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:246: warning - @param argument "stopCodonSequence" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/AbstractFeature.java:67: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/AbstractFeature.java:87: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/AbstractFeature.java:106: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/AbstractFeature.java:134: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/AbstractFeature.java:143: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/FeatureInterface.java:31: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/FeatureInterface.java:45: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/FeatureInterface.java:53: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/FeatureInterface.java:122: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/FeatureInterface.java:129: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/FeatureInterface.java:53: warning - @return tag cannot be used in method with void return type. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/features/FeaturesKeyWordInterface.java:39: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/BufferedReaderBytesRead.java:102: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/ProteinSequenceCreator.java:58: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/ProteinSequenceCreator.java:67: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/ProteinSequenceCreator.java:80: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/template/SequenceCreatorInterface.java:42: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/template/SequenceCreatorInterface.java:49: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/template/SequenceCreatorInterface.java:55: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/DNASequenceCreator.java:60: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/DNASequenceCreator.java:70: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/DNASequenceCreator.java:80: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaReader.java:66: warning - @param argument "br" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaReader.java:133: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:52: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:79: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:95: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:110: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:125: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/template/SequenceParserInterface.java:39: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaWriterHelper.java:172: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FastaWriterHelper.java:103: warning - @param argument "dnaSequences" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:76: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:92: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:102: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:60: warning - @param argument "fastaFile" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FileProxyProteinSequenceCreator.java:73: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FileProxyProteinSequenceCreator.java:91: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FileProxyProteinSequenceCreator.java:101: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/FileProxyProteinSequenceCreator.java:59: warning - @param argument "fastaFile" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenbankReader.java:67: warning - @param argument "br" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenbankReader.java:133: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenbankReaderHelper.java:52: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenbankReaderHelper.java:80: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenbankReaderHelper.java:106: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenbankReaderHelper.java:122: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenbankReaderHelper.java:137: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenbankReaderHelper.java:152: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/template/FastaHeaderFormatInterface.java:38: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericFastaHeaderParser.java:67: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:88: warning - @inheritDoc used but setAccession(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:123: warning - @inheritDoc used but setComment(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:96: warning - @inheritDoc used but setDescription(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:105: warning - @inheritDoc used but setIdentifier(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:114: warning - @inheritDoc used but setName(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:71: warning - @inheritDoc used but setVersion(int) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:71: warning - @inheritDoc used but setVersion(int) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:88: warning - @inheritDoc used but setAccession(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:96: warning - @inheritDoc used but setDescription(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:105: warning - @inheritDoc used but setIdentifier(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:114: warning - @inheritDoc used but setName(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:123: warning - @inheritDoc used but setComment(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/IUPACParser.java:273: warning - @param argument "nucleotides" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/PlainFastaHeaderParser.java:48: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/RNASequenceCreator.java:40: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/RNASequenceCreator.java:49: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/RNASequenceCreator.java:58: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/template/SequenceParserInterface.java:39: warning - @param argument "dataInput" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/util/IOUtils.java:196: warning - Tag @link: can't find processReader(String) in org.biojava3.core.sequence.io.util.IOUtils [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:88: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:99: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:109: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:118: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:127: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:136: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:144: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:152: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:168: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:227: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:235: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:244: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:253: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/GenbankProxySequenceReader.java:151: warning - @param argument "aGenbankDirectoryCache" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:142: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:151: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:163: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:175: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:186: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:197: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:208: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:221: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:235: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:246: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:257: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:279: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:288: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:297: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:99: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:131: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:140: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:149: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:158: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:167: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:175: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:183: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:192: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:203: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:214: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:222: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:230: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:238: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:259: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:402: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:424: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:446: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:466: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:269: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:339: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/location/LocationHelper.java:59: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/location/LocationHelper.java:122: warning - @param argument "location" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/location/template/Location.java:78: warning - Tag @link: can't find getAllSubLocations() in org.biojava3.core.sequence.location.template.Location [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/location/template/Location.java:114: warning - @param argument "<C>" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/location/template/Location.java:125: warning - @param argument "<C>" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/location/template/Location.java:176: warning - @param argument "location" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/SequenceAsStringHelper.java:28: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:146: warning - Tag @link: can't find countCompounds(org.biojava3.core.sequence.template.Sequence, C[]) in org.biojava3.core.sequence.template.SequenceMixin [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:144: warning - @param argument "bioBegin" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:162: warning - @param argument "bioEnd" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:194: warning - @param argument "annotation" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:331: warning - @param argument "featureType" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:469: warning - @param argument "species" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @param argument "begin" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @param argument "end" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:237: warning - Tag @link: reference not found: SequenceBackingStore [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:156: warning - Tag @link: can't find toString() in org.biojava3.core.sequence.template.Compound [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:144: warning - @param argument "writer" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:237: warning - Tag @link: reference not found: SequenceBackingStore [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/Table.java:39: warning - Tag @link: reference not found: IUPACTable [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:62: warning - @ is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:62: warning - @link{AminoAcidCompound is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:62: warning - @ is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:62: warning - @link{AminoAcidCompound is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:175: warning - Tag @link: reference not found: TranslationEngine [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:74: warning - @ is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:74: warning - @ is an unknown tag. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:175: warning - Tag @link: reference not found: TranslationEngine [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/util/InputStreamProvider.java:242: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/util/StringManipulationHelper.java:73: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/util/StringManipulationHelper.java:73: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/genome/GeneFeatureHelper.java:181: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/genome/GeneFeatureHelper.java:331: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/genome/parsers/gff/FeatureHelper.java:24: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/genome/parsers/gff/GFF3Writer.java:33: warning - @param argument "fileName" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/genome/parsers/gff/GFF3Writer.java:33: warning - @param argument "chromosomeSequence" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/phylo/Comparison.java:24: warning - @param argument "s1" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/phylo/Comparison.java:24: warning - @param argument "s2" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/Component.java:43: warning - Tag @link: reference not found: register [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/Component.java:43: warning - Tag @link: reference not found: of [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/Component.java:122: warning - @param argument "pdbccIds" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/ModificationLinkage.java:63: warning - @param argument "labelOfAtomOnComponent1" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/ModificationLinkage.java:63: warning - @param argument "labelOfAtomOnComponent2" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/ModificationLinkage.java:86: warning - @param argument "labelOfAtomOnComponent1" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/ModificationLinkage.java:86: warning - @param argument "labelOfAtomOnComponent2" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/ProteinModificationRegistry.java:212: warning - @param argument "mod" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:79: warning - Tag @see: can't find getLinkedGroupPairs in org.biojava3.protmod.structure.ModifiedCompound [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:85: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:52: warning - Tag @link: reference not found: ProteinModificationBean [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:85: warning - @return tag cannot be used in method with void return type. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:93: warning - Tag @link: reference not found: addGroup [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ModifiedCompoundImpl.java:77: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:52: warning - Tag @link: reference not found: ProteinModificationBean [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:93: warning - Tag @link: reference not found: addGroup [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/ProteinModificationIdentifier.java:124: warning - @param argument "recordUnidentifiableAtomLinkages" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/protmod/structure/StructureUtil.java:282: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ronn/Jronn.java:157: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ronn/Jronn.java:261: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ronn/Jronn.java:278: warning - Tag @see: can't find Jronn.Range in org.biojava3.ronn.Jronn [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "58" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "47" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "47" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "47" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "47" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "47" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "63" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "61" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "47" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "45" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "45" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link:illegal character: "47" in "http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:77: warning - Tag @link: can't find setStrictSCOP(boolean) in org.biojava3.structure.StructureIO [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/structure/StructureIO.java:108: warning - Tag @link: reference not found: http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/BlastJob.java:40: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:154: warning - Tag @link: can't find printRemoteBlastInfo() in org.biojava3.ws.alignment.qblast.NCBIQBlastService [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:154: warning - @param argument "db" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:177: warning - @param argument "expect:" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:225: warning - @param argument "word:" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:377: warning - #DEFAULT_TOOL (referenced by @value tag) is an unknown reference. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:386: warning - #DEFAULT_TOOL (referenced by @value tag) is an unknown reference. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:395: warning - #DEFAULT_EMAIL (referenced by @value tag) is an unknown reference. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:404: warning - #DEFAULT_EMAIL (referenced by @value tag) is an unknown reference. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:53: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:150: warning - Tag @see: can't find infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) in org.forester.sdi.SDIR [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "[args[0]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "[args[0]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "[args[0]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "[args[0]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "[args[0]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "args[0or1]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "args[1or2]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "args[2or3]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "args[3or4]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/sdi_dir.java:393: warning - @param argument "args[4or5]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/support_transfer.java:66: warning - @param argument "args[0]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/support_transfer.java:66: warning - @param argument "args[1]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/support_transfer.java:66: warning - @param argument "args[2]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/application/support_transfer.java:66: warning - @param argument "args[3]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:324: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:354: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java:110: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/evoinference/distance/PairwiseDistanceCalculator.java:74: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/evoinference/parsimony/FitchParsimony.java:153: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/evoinference/parsimony/SankoffParsimony.java:160: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/go/GoUtils.java:61: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/io/parsers/HmmPfamOutputParser.java:633: warning - @param argument "ignored_engulfed_domains" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/io/parsers/HmmscanPerDomainTableParser.java:576: warning - @param argument "ignored_engulfed_domains" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/io/parsers/nhx/NHXParser.java:264: warning - Tag @see: can't find setSource( final Object nhx_source ) in org.forester.io.parsers.nhx.NHXParser [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/io/parsers/util/ParserUtils.java:104: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/io/parsers/util/ParserUtils.java:227: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/io/parsers/util/PhylogenyParserException.java:50: warning - @param argument "arg0" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:58: warning - @param argument "annotate_phylogeny" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/Phylogeny.java:90: warning - @param argument "n" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/PhylogenyMethods.java:851: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/PhylogenyMethods.java:170: warning - @param argument "n" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/PhylogenyNode.java:106: warning - Tag @see: missing '#': "addAsChild( PhylogenyNode n )" [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/PhylogenyNode.java:106: warning - Tag @see: can't find addAsChild( PhylogenyNode n ) in org.forester.phylogeny.PhylogenyNode [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/PhylogenyNode.java:92: warning - @param argument "n" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/PhylogenyNode.java:285: warning - @param argument "n" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/PhylogenyNode.java:814: warning - @param argument "n" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/data/PhylogenyData.java:59: warning - @param argument "PhylogenyData" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/iterators/ExternalForwardIterator.java:48: warning - @param argument "tree" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/phylogeny/iterators/PostorderTreeIterator.java:48: warning - @param argument "t" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/protein/Protein.java:49: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/ORcount.java:345: warning - @param argument "args[1or2]" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/RIO.java:423: warning - Tag @see: can't find inferOrthologs(Phylogeny[],Phylogeny) in org.forester.sdi.RIO [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/RIO.java:423: warning - Tag @see: can't find inferOrthologs(File,Phylogeny) in org.forester.sdi.RIO [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/SDIR.java:83: warning - Tag @see: can't find infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) in org.forester.sdi.SDIR [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/SDIR.java:105: warning - Tag @see: can't find infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) in org.forester.sdi.SDIR [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/SDIR.java:120: warning - Tag @see: can't find infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) in org.forester.sdi.SDIR [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/SDIR.java:133: warning - Tag @see: can't find infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) in org.forester.sdi.SDIR [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/SDIR.java:149: warning - Tag @see: can't find infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) in org.forester.sdi.SDIR [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/sdi/SDIse.java:84: warning - Tag @see: can't find infer(boolean) in org.forester.sdi.SDIse [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java:158: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/DomainLengths.java:70: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/DomainLengths.java:86: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/DomainParsimonyCalculator.java:556: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/DomainSimilarity.java:56: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/SurfacingUtil.java:1282: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/SurfacingUtil.java:1421: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/SurfacingUtil.java:761: warning - @param argument "consider_directedness_and_adjacency_for_bin_combinations" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/surfacing/SurfacingUtil.java:761: warning - @param argument "all_binary_domains_combination_gained" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/tools/TreeSplitMatrix.java:77: warning - @param argument "target" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/util/DescriptiveStatistics.java:46: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/util/DescriptiveStatistics.java:74: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/ws/seqdb/SequenceDbWsTools.java:76: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/ws/seqdb/SequenceDbWsTools.java:76: warning - @param argument "db" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/ws/seqdb/UniProtTaxonomy.java:173: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/ws/uniprot/SequenceDbWsTools.java:76: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/ws/uniprot/SequenceDbWsTools.java:76: warning - @param argument "db" is not a parameter name. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/forester/ws/uniprot/UniProtTaxonomy.java:173: warning - @return tag has no arguments. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:66: warning - Tag @link: reference not found: FastaSequence FastaSequences [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/Table.java:39: warning - Tag @link: reference not found: IUPACTable [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:175: warning - Tag @link: reference not found: TranslationEngine [javadoc] Building index for all the packages and classes... [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:87: warning - Tag @link: reference not found: cpSite [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:110: warning - Tag @link: reference not found: cpSite [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/io/FastaAFPChainConverter.java:66: warning - Tag @link: reference not found: FastaSequence FastaSequences [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:88: warning - @inheritDoc used but setAccession(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:123: warning - @inheritDoc used but setComment(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:96: warning - @inheritDoc used but setDescription(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:105: warning - @inheritDoc used but setIdentifier(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:114: warning - @inheritDoc used but setName(String) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java:71: warning - @inheritDoc used but setVersion(int) does not override or implement any method. [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:237: warning - Tag @link: reference not found: SequenceBackingStore [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Calc.java:146: warning - Tag @link: reference not found: subtract [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/Table.java:39: warning - Tag @link: reference not found: IUPACTable [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:175: warning - Tag @link: reference not found: TranslationEngine [javadoc] Building index for all classes... [javadoc] Generating /build/buildd/biojava3-live-3.0.7+dfsg/doc/biojava/help-doc.html... [javadoc] 575 warnings [javadoc] /build/buildd/biojava3-live-3.0.7+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Calc.java:146: warning - Tag @link: reference not found: subtract BUILD SUCCESSFUL Total time: 25 seconds rm -rf biojavadoc make[1]: Leaving directory `/build/buildd/biojava3-live-3.0.7+dfsg' jh_build debian/rules override_dh_auto_test make[1]: Entering directory `/build/buildd/biojava3-live-3.0.7+dfsg' cd biojava3-core && ant test Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-core/build.xml compile-test: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-core/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-core/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 16 source files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-core/classes [javac] Note: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-core/src/test/java/org/biojava3/core/sequence/DNATest.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 8 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-core/classes [copy] Copying 134 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-core/classes test: [junit] Running org.biojava3.core.sequence.DNATest [junit] Testsuite: org.biojava3.core.sequence.DNATest [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 sec [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 sec [junit] [junit] Testcase: sequenceEquality took 0.012 sec [junit] Testcase: subSequence took 0.003 sec [junit] Testcase: singleCompoundSequence took 0.001 sec [junit] Testcase: translateToRna took 0.029 sec [junit] Testcase: kmerNonOverlap took 0.001 sec [junit] Testcase: twoBit took 0 sec [junit] Testcase: composition took 0 sec [junit] Testcase: fourBit took 0.002 sec [junit] Testcase: complement took 0.001 sec [junit] Testcase: kmerOverlapExceedingSequenceLength took 0 sec [junit] Testcase: at took 0 sec [junit] Testcase: gc took 0.001 sec [junit] Testcase: basesEqual took 0 sec [junit] Testcase: bogusSequence took 0 sec [junit] Testcase: kmerOverlap took 0 sec [junit] Testcase: reverseComplement took 0.001 sec [junit] Testcase: reverse took 0 sec [junit] Testcase: respectCase took 0 sec [junit] Testcase: basesEquivalent took 0 sec [junit] Testcase: badTwoBit took 0.001 sec [junit] Running org.biojava3.core.sequence.EditSequenceTest [junit] Testsuite: org.biojava3.core.sequence.EditSequenceTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec [junit] [junit] Testcase: badSubstitute took 0.013 sec [junit] Testcase: delete took 0.004 sec [junit] Testcase: insert took 0.001 sec [junit] Testcase: substitute took 0.001 sec [junit] Running org.biojava3.core.sequence.JoiningSequenceReaderTest [junit] Testsuite: org.biojava3.core.sequence.JoiningSequenceReaderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec [junit] [junit] Testcase: empty took 0.012 sec [junit] Testcase: canScan took 0.001 sec [junit] Running org.biojava3.core.sequence.MultipleSequenceAlignmentTest [junit] Testsuite: org.biojava3.core.sequence.MultipleSequenceAlignmentTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] [junit] Testcase: testGetCompoundsAt took 0.015 sec [junit] Running org.biojava3.core.sequence.SequenceViewTest [junit] Testsuite: org.biojava3.core.sequence.SequenceViewTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec [junit] [junit] Testcase: testLastIndexOf took 0.014 sec [junit] Testcase: testGetCompoundAt took 0 sec [junit] Testcase: testInverse took 0 sec [junit] Running org.biojava3.core.sequence.TranslationTest [junit] Testsuite: org.biojava3.core.sequence.TranslationTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.406 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.406 sec [junit] [junit] Testcase: translateN took 0.031 sec [junit] Testcase: basicTranslation took 0.001 sec [junit] Testcase: translateBrca2 took 0.303 sec [junit] Testcase: getUniversal took 0 sec [junit] Testcase: translateInternalStops took 0.01 sec [junit] Testcase: multiFrameTranslation took 0.003 sec [junit] Testcase: translateInitMet took 0 sec [junit] Testcase: lowerCases took 0 sec [junit] Testcase: testHashCollision took 0 sec [junit] Testcase: translateBrca2ExonOne took 0.001 sec [junit] Running org.biojava3.core.sequence.compound.AmbiguityDNACompoundTest [junit] Testsuite: org.biojava3.core.sequence.compound.AmbiguityDNACompoundTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] [junit] Testcase: testAmbiguity took 0.001 sec [junit] Testcase: testBasicAmbiguity took 0 sec [junit] Running org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreatorTest [junit] Testsuite: org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreatorTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] [junit] Testcase: testConstructor took 0.011 sec [junit] Running org.biojava3.core.sequence.io.FastaReaderTest [junit] Testsuite: org.biojava3.core.sequence.io.FastaReaderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 sec [junit] ------------- Standard Output --------------- [junit] process [junit] process(int) [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testProcess took 0.097 sec [junit] Testcase: processIntTest took 0.031 sec [junit] Running org.biojava3.core.sequence.io.FastaWriterTest [junit] Testsuite: org.biojava3.core.sequence.io.FastaWriterTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec [junit] [junit] Testcase: writeBasicFasta took 0.018 sec [junit] Testcase: writeFastaEqualToLineLength took 0 sec [junit] Running org.biojava3.core.sequence.io.GenbankCookbookTest [junit] Testsuite: org.biojava3.core.sequence.io.GenbankCookbookTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 sec [junit] ------------- Standard Output --------------- [junit] AAGATGCTCCGTGGAAGGGAGCCGAGCGGTGGGCAGAGGCTGAGTCCCCGATAACGAGCGCCTCACATTTCCGTGGCATTCCCATTTGCTAGTGCGCTGCTGCGGCCGCACGCCTGATTGATATATGACTGCAATGGCACTTTTCCATTTGACATTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCCCTCTCTCTCTCCCTCTCTCTCTCTCCCTGTGTCGCTTAAACAACAGTCCTAACTTTTGTGTGTTGCAAATATAAAAGGCAAGCCATGTGACAGAGGGACAGAAGAACAAAAGCATTTGGAAGTAACAGGACCTCTTTCTAGCTCTCAGAAAAGTCTGAGAAGAAAGGAGCCCTGCGTTCCCCTAAGCTGTGCAGCAGATACTGTGATGATGGATTGCAAGTGCAAAGAGTAAGACAAAACTCCAGCACATAAAGGACAATGACAACCAGAAAGCTTCAGCCCGATCCTGCCCTTTCCTTGAACGGGACTGGATCCTAGGAGGTGAAGCCATTTCCAATTTTTTGTCCTCTGCCTCCCTCTGCTGTTCTTCTAGAGAAGTTTTTCCTTACAACAATGAGAAAACATGTACTAGCTGCATCCTTTTCTATGCTCTCCCTGCTGGTGATAATGGGAGATACAGACAGTAAAACGGACAGCTCATTCATAATGGACTCGGACCCTCGACGCTGCATGAGGCACCACTATGTGGATTCTATCAGTCACCCATTGTACAAGTGTAGCTCAAAGATGGTGCTCCTGGCCAGGTGCGAGGGGCACTGCAGCCAGGCGTCACGCTCCGAGCCTTTGGTGTCGTTCAGCACTGTCCTCAAGCAACCCTTCCGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCTGAAGGCACTGCGGCTGCGATGCTCAGGGGGCATGCGACTCACTGCCACCTACCGGTACATCCTCTCCTGTCACTGCGAGGAATGCAATTCCTGAGGCCCGCTGCTGTGTGTGGCTTCTGGATGGGACAACTGTAGAGGCAGTTCGACCAGCCAGGGAAAGACTGGCAAGAAAAGAGTTAAGGCAAAAAAGGATGCAACAATTCTCCCGGGACTCTGCATATTCTAGTAATAAAGACTCTACATGCTTGTTGACAGAGAGAGATACTCTGGGAACTTCTTTGCAGTTCCCATCTCCTTTCTCTGGTACAATTTCTTTTGGTTCATTTTCAGATTCAGGCATTTTCCCCCTTGGCTCTCAATGCTGTTTGGGTTTCCAACAATTCAGCATTAGTGGGAAAAAGTGGGCCCTCATACACAAGCGTGTCAGGCTGTCAGTGTTTGGTGCACGCTGGGGAAGAATTTACTTTGGAAAGTAGAAAAGCCCAGCTTTTCCTGGGACATCTTCTGTTATTGTTGATGTTTTTTTTTACCTTGTCATTTTGGTCTAAGGTTGCCATTGCTGCTAAAGGTTACCGATTTCAAAGTCCAGATACCAAGCATGTGGATATGTTTAGCTACGTTTACTCACAGCCAGCGAACTGACATTAAAATAACTAACAAACAGATTCTTTTATGTGATGCTGGAACTCTTGACAGCTATAATTATTATTCAGAAATGACTTTTTGAAAGTAAAAGCAGCATAAAGAATTTGTCACAGGAAGGCTGTCTCAGATAAATTATGGTAAAATTTTGTAAGGGAGCAGACTTTTAAAGACTTGCACAAATACGGATCCTGCACTGACTCTGGAAAAGGCATATATGTACTAGTGGCATGGAGAATGCACCATACTCATGCATGCAAATTAGACAACCAAGTATGAATCTATTTGTGGGTGTGCTATAGCTTTAGCCGTGTCACGGGCATCATTCTCTAATATCCACTTGTCCATGTGAAACATGTTGCCAAAATGGTGGCCTGGCTTGTCTTCTGAACGTTTGGTTCAAATGTGTTTTGGTCCTGGAGGCTCAAATTTTGAGTTATTCCCACGTTTTGAAATAAAAAGAGTATATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA [junit] MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS [junit] {NM_000266=AAGATGCTCCGTGGAAGGGAGCCGAGCGGTGGGCAGAGGCTGAGTCCCCGATAACGAGCGCCTCACATTTCCGTGGCATTCCCATTTGCTAGTGCGCTGCTGCGGCCGCACGCCTGATTGATATATGACTGCAATGGCACTTTTCCATTTGACATTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCCCTCTCTCTCTCCCTCTCTCTCTCTCCCTGTGTCGCTTAAACAACAGTCCTAACTTTTGTGTGTTGCAAATATAAAAGGCAAGCCATGTGACAGAGGGACAGAAGAACAAAAGCATTTGGAAGTAACAGGACCTCTTTCTAGCTCTCAGAAAAGTCTGAGAAGAAAGGAGCCCTGCGTTCCCCTAAGCTGTGCAGCAGATACTGTGATGATGGATTGCAAGTGCAAAGAGTAAGACAAAACTCCAGCACATAAAGGACAATGACAACCAGAAAGCTTCAGCCCGATCCTGCCCTTTCCTTGAACGGGACTGGATCCTAGGAGGTGAAGCCATTTCCAATTTTTTGTCCTCTGCCTCCCTCTGCTGTTCTTCTAGAGAAGTTTTTCCTTACAACAATGAGAAAACATGTACTAGCTGCATCCTTTTCTATGCTCTCCCTGCTGGTGATAATGGGAGATACAGACAGTAAAACGGACAGCTCATTCATAATGGACTCGGACCCTCGACGCTGCATGAGGCACCACTATGTGGATTCTATCAGTCACCCATTGTACAAGTGTAGCTCAAAGATGGTGCTCCTGGCCAGGTGCGAGGGGCACTGCAGCCAGGCGTCACGCTCCGAGCCTTTGGTGTCGTTCAGCACTGTCCTCAAGCAACCCTTCCGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCTGAAGGCACTGCGGCTGCGATGCTCAGGGGGCATGCGACTCACTGCCACCTACCGGTACATCCTCTCCTGTCACTGCGAGGAATGCAATTCCTGAGGCCCGCTGCTGTGTGTGGCTTCTGGATGGGACAACTGTAGAGGCAGTTCGACCAGCCAGGGAAAGACTGGCAAGAAAAGAGTTAAGGCAAAAAAGGATGCAACAATTCTCCCGGGACTCTGCATATTCTAGTAATAAAGACTCTACATGCTTGTTGACAGAGAGAGATACTCTGGGAACTTCTTTGCAGTTCCCATCTCCTTTCTCTGGTACAATTTCTTTTGGTTCATTTTCAGATTCAGGCATTTTCCCCCTTGGCTCTCAATGCTGTTTGGGTTTCCAACAATTCAGCATTAGTGGGAAAAAGTGGGCCCTCATACACAAGCGTGTCAGGCTGTCAGTGTTTGGTGCACGCTGGGGAAGAATTTACTTTGGAAAGTAGAAAAGCCCAGCTTTTCCTGGGACATCTTCTGTTATTGTTGATGTTTTTTTTTACCTTGTCATTTTGGTCTAAGGTTGCCATTGCTGCTAAAGGTTACCGATTTCAAAGTCCAGATACCAAGCATGTGGATATGTTTAGCTACGTTTACTCACAGCCAGCGAACTGACATTAAAATAACTAACAAACAGATTCTTTTATGTGATGCTGGAACTCTTGACAGCTATAATTATTATTCAGAAATGACTTTTTGAAAGTAAAAGCAGCATAAAGAATTTGTCACAGGAAGGCTGTCTCAGATAAATTATGGTAAAATTTTGTAAGGGAGCAGACTTTTAAAGACTTGCACAAATACGGATCCTGCACTGACTCTGGAAAAGGCATATATGTACTAGTGGCATGGAGAATGCACCATACTCATGCATGCAAATTAGACAACCAAGTATGAATCTATTTGTGGGTGTGCTATAGCTTTAGCCGTGTCACGGGCATCATTCTCTAATATCCACTTGTCCATGTGAAACATGTTGCCAAAATGGTGGCCTGGCTTGTCTTCTGAACGTTTGGTTCAAATGTGTTTTGGTCCTGGAGGCTCAAATTTTGAGTTATTCCCACGTTTTGAAATAAAAAGAGTATATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA} [junit] {NP_000257=MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS} [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testProcess took 0.098 sec [junit] Running org.biojava3.core.sequence.io.GenbankReaderTest [junit] Testsuite: org.biojava3.core.sequence.io.GenbankReaderTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec [junit] ------------- Standard Output --------------- [junit] process protein [junit] process DNA [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testProcess took 0.07 sec [junit] Running org.biojava3.core.sequence.io.GenericFastaHeaderParserTest [junit] Testsuite: org.biojava3.core.sequence.io.GenericFastaHeaderParserTest [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] ------------- Standard Output --------------- [junit] parseHeader [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testParseHeader took 0.01 sec [junit] Running org.biojava3.core.sequence.location.LocationParserTest [junit] Testsuite: org.biojava3.core.sequence.location.LocationParserTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] [junit] Testcase: moreComplex took 0.008 sec [junit] Testcase: basicLocationTests took 0.001 sec [junit] Running org.biojava3.core.sequence.location.LocationTest [junit] Testsuite: org.biojava3.core.sequence.location.LocationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec [junit] [junit] Testcase: testWithStrandSwitch took 0.017 sec [junit] Testcase: modulateCircular took 0.001 sec [junit] Testcase: testStrandFlip took 0.001 sec [junit] Testcase: testBasicCircularLocation took 0.001 sec [junit] Testcase: badLocations took 0.001 sec [junit] Testcase: completePasses took 0 sec [junit] Testcase: testSubLocations took 0.001 sec BUILD SUCCESSFUL Total time: 7 seconds cd biojava3-alignment && ant test Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-alignment/build.xml compile-test: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-alignment/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-alignment/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 22 source files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-alignment/classes [copy] Copying 9 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-alignment/classes [copy] Copying 65 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-alignment/classes test: [junit] Running org.biojava3.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava3.alignment.FractionalIdentityScorerTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] [junit] Testcase: testGetQuery took 0.022 sec [junit] Testcase: testGetScore took 0.015 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0 sec [junit] Running org.biojava3.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava3.alignment.FractionalSimilarityScorerTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] [junit] Testcase: testGetQuery took 0.023 sec [junit] Testcase: testGetScore took 0.015 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0 sec [junit] Running org.biojava3.alignment.GuideTreeTest [junit] Testsuite: org.biojava3.alignment.GuideTreeTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 sec [junit] [junit] Testcase: testGuideTree took 0.067 sec [junit] Testcase: testToString took 0.002 sec [junit] Testcase: testGetScoreMatrix took 0.003 sec [junit] Testcase: testGetRoot took 0.017 sec [junit] Testcase: testGetSequences took 0.003 sec [junit] Testcase: testGetDistanceMatrix took 0.002 sec [junit] Testcase: testGetAllPairsScores took 0.002 sec [junit] Testcase: testIterator took 0.002 sec [junit] Running org.biojava3.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava3.alignment.NeedlemanWunschTest [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.022 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.015 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.003 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.012 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava3.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava3.alignment.SimpleAlignedSequenceTest [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 sec [junit] [junit] Testcase: testGetIndexOf took 0.011 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetNumGaps took 0.001 sec [junit] Testcase: testGetStart took 0 sec [junit] Testcase: testGetSequenceIndexAt took 0 sec [junit] Testcase: testGetAccession took 0 sec [junit] Testcase: testToString took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0 sec [junit] Testcase: testCountCompounds took 0 sec [junit] Testcase: testGetAlignmentIndexAt took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.001 sec [junit] Testcase: testGetOriginalSequence took 0 sec [junit] Testcase: testGetCompoundAt took 0 sec [junit] Testcase: testGetLength took 0 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetEnd took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceLocal took 0 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0 sec [junit] Testcase: testGetOverlapCount took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetLocationInAlignment took 0.001 sec [junit] Testcase: testIterator took 0 sec [junit] Testcase: testGetSequenceAsString took 0 sec [junit] Testcase: testGetLastIndexOf took 0 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.001 sec [junit] Running org.biojava3.alignment.SimpleGapPenaltyTest [junit] Testsuite: org.biojava3.alignment.SimpleGapPenaltyTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] [junit] Testcase: testOpenPenalty took 0.001 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.biojava3.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava3.alignment.SimpleProfilePairTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec [junit] [junit] Testcase: testGetQuery took 0.04 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testSimpleProfilePair took 0.003 sec [junit] Running org.biojava3.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava3.alignment.SimpleProfileProfileAlignerTest [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.039 sec [junit] Testcase: testGetGapPenalty took 0.003 sec [junit] Testcase: testGetComputationTime took 0.004 sec [junit] Testcase: testGetQuery took 0.002 sec [junit] Testcase: testGetScore took 0.002 sec [junit] Testcase: testGetScoreMatrix took 0.002 sec [junit] Testcase: testGetPair took 0.004 sec [junit] Testcase: testGetProfile took 0.003 sec [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec [junit] Testcase: testGetScoreMatrixAsString took 0.02 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.001 sec [junit] Testcase: testSimpleProfileProfileAligner took 0.002 sec [junit] Testcase: testGetTarget took 0.002 sec [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava3.alignment.SimpleProfileTest [junit] Testsuite: org.biojava3.alignment.SimpleProfileTest [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.104 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.104 sec [junit] [junit] Testcase: testGetIndexOf took 0.027 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequenceInt took 0.001 sec [junit] Testcase: testToStringInt took 0.007 sec [junit] Testcase: testToString took 0.001 sec [junit] Testcase: testToStringFormatted took 0.019 sec [junit] Testcase: testSimpleProfile took 0 sec [junit] Testcase: testGetSize took 0 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec [junit] Testcase: testGetAlignedSequences took 0 sec [junit] Testcase: testGetOriginalSequences took 0.001 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0 sec [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec [junit] Testcase: testGetIndicesAt took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.001 sec [junit] Testcase: testGetCompoundAtIntInt took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetCompoundsAt took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec [junit] Testcase: testIterator took 0 sec [junit] Testcase: testGetLastIndexOf took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0 sec [junit] Running org.biojava3.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava3.alignment.SimpleSequencePairTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.027 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetIndexInTargetAt took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetCompoundInQueryAt took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumIdenticals took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAt took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumSimilars took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0 sec [junit] Running org.biojava3.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava3.alignment.SimpleSubstitutionMatrixTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.058 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.058 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.005 sec [junit] Testcase: testSetDescription took 0.011 sec [junit] Testcase: testToString took 0.007 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.006 sec [junit] Testcase: testSimpleSubstitutionMatrixWrong took 0 sec [junit] SKIPPED [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.002 sec [junit] Testcase: testSetName took 0.006 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.002 sec [junit] Running org.biojava3.alignment.SmithWatermanTest [junit] Testsuite: org.biojava3.alignment.SmithWatermanTest [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.022 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.016 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0.002 sec [junit] Testcase: testGetPair took 0.004 sec [junit] Testcase: testSmithWaterman took 0.001 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.027 sec [junit] Testcase: testSetStoringScoreMatrix took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava3.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava3.alignment.routines.GuanUberbacherTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 sec [junit] [junit] Testcase: testGetComputationTime took 0.036 sec [junit] Testcase: testGuanUberbacher took 0.001 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testGetPair took 0.003 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testGetMaxScore took 0 sec BUILD SUCCESSFUL Total time: 6 seconds cd biojava3-aa-prop && ant test Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-aa-prop/build.xml compile-test: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-aa-prop/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-aa-prop/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 9 source files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-aa-prop/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 12 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-aa-prop/classes [copy] Copying 31 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-aa-prop/classes test: BUILD SUCCESSFUL Total time: 1 second # Skip, missing dependency #cd biojava3-genome && ant test cd biojava3-phylo && ant test Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-phylo/build.xml compile-test: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-phylo/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-phylo/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 1 source file to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-phylo/classes [copy] Warning: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-phylo/src/test/resources does not exist. [copy] Copying 10 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-phylo/classes test: [junit] Running org.biojava3.phylo.AppTest [junit] Testsuite: org.biojava3.phylo.AppTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] [junit] Testcase: testApp took 0.001 sec BUILD SUCCESSFUL Total time: 1 second # Native errors may cause issue on NFS...; skipping #cd biojava3-sequencing && ant test #cd biojava3-modfinder && ant test cd biojava3-protein-disorder && ant test Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-protein-disorder/build.xml compile-test: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-protein-disorder/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-protein-disorder/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 3 source files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-protein-disorder/classes [copy] Copying 1 file to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-protein-disorder/classes [copy] Copying 14 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-protein-disorder/classes test: [junit] Running org.biojava3.ronn.JronnTest [junit] Testsuite: org.biojava3.ronn.JronnTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.009 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.009 sec [junit] [junit] Testcase: verifyRanges took 1.996 sec [junit] Running org.biojava3.ronn.NonstandardProteinCompoundTest [junit] Testsuite: org.biojava3.ronn.NonstandardProteinCompoundTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] [junit] Testcase: test took 0 sec BUILD SUCCESSFUL Total time: 3 seconds # Requires remote access and tmp directory write access #cd biojava3-structure && ant test cd biojava3-structure-gui && ant test Buildfile: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-structure-gui/build.xml compile-test: [mkdir] Created dir: /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-structure-gui/classes [javac] /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-structure-gui/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 6 source files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-structure-gui/classes [copy] Warning: /build/buildd/biojava3-live-3.0.7+dfsg/biojava3-structure-gui/src/test/resources does not exist. [copy] Copying 111 files to /build/buildd/biojava3-live-3.0.7+dfsg/buildtest/biojava3-structure-gui/classes test: [junit] Running org.biojava.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.structure.gui.JmolViewerImplTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] [junit] Testcase: testMe took 0 sec [junit] Running org.biojava.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.structure.gui.RenderStyleTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] [junit] Testcase: testSomeMethod took 0.001 sec [junit] Running org.biojava.structure.gui.StructureViewerTest [junit] Testsuite: org.biojava.structure.gui.StructureViewerTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] [junit] Testcase: testGetColor took 0.002 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec [junit] Testcase: testGetSelection took 0.003 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.structure.gui.ViewerTest [junit] Testsuite: org.biojava.structure.gui.ViewerTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] [junit] Testcase: testStructureLoad took 0 sec BUILD SUCCESSFUL Total time: 2 seconds #No test in biojava-ws available #cd biojava3-ws && ant test make[1]: Leaving directory `/build/buildd/biojava3-live-3.0.7+dfsg' /usr/bin/fakeroot debian/rules binary dh binary --with javahelper dh_testroot dh_prep dh_auto_install dh_install jh_installjavadoc dh_installdocs dh_installchangelogs dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_exec jh_depends dh_compress dh_fixperms dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libbiojava3.0-java: unknown substitution variable ${shlibs:Depends} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package libbiojava3.0-java: unused substitution variable ${java:Depends} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums dh_builddeb INFO: pkgstriptranslations version 119 pkgstriptranslations: processing libbiojava3.0-java (in debian/libbiojava3.0-java); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbiojava3.0-java/DEBIAN/control, package libbiojava3.0-java, directory debian/libbiojava3.0-java pkgstripfiles: PNG optimization for package libbiojava3.0-java took 0 s dpkg-deb: warning: 'debian/libbiojava3.0-java/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `libbiojava3.0-java' in `../libbiojava3.0-java_3.0.7+dfsg-1_all.deb'. INFO: pkgstriptranslations version 119 pkgstriptranslations: processing libbiojava3-java (in debian/libbiojava3-java); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbiojava3-java/DEBIAN/control, package libbiojava3-java, directory debian/libbiojava3-java Searching for duplicated docs in dependency libbiojava3.0-java... symlinking changelog.Debian.gz in libbiojava3-java to file in libbiojava3.0-java pkgstripfiles: PNG optimization for package libbiojava3-java took 0 s dpkg-deb: warning: 'debian/libbiojava3-java/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `libbiojava3-java' in `../libbiojava3-java_3.0.7+dfsg-1_all.deb'. INFO: pkgstriptranslations version 119 pkgstriptranslations: processing libbiojava3-java-doc (in debian/libbiojava3-java-doc); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbiojava3-java-doc/DEBIAN/control, package libbiojava3-java-doc, directory debian/libbiojava3-java-doc pkgstripfiles: Disabled PNG optimization for -doc package libbiojava3-java-doc (to save build time) dpkg-deb: warning: 'debian/libbiojava3-java-doc/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `libbiojava3-java-doc' in `../libbiojava3-java-doc_3.0.7+dfsg-1_all.deb'. dpkg-genchanges -b -mUbuntu/amd64 Build Daemon >../biojava3-live_3.0.7+dfsg-1_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build biojava3-live-3.0.7+dfsg dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20140203-1715 chroot-autobuild/build/buildd/libbiojava3.0-java_3.0.7+dfsg-1_all.deb: new debian package, version 2.0. size 3574170 bytes: control archive= 1325 bytes. 1226 bytes, 21 lines control 1171 bytes, 15 lines md5sums Package: libbiojava3.0-java Source: biojava3-live Version: 3.0.7+dfsg-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3744 Depends: libcommons-pool-java (>= 1.1), libcommons-collections-java (>= 2.1), libcommons-dbcp-java (>= 1.1), libcommons-logging-java, libhsqldb-java, libbytecode-java, icedtea-netx, libjson-simple-java, libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java, liblog4j1.2-java Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc Section: java Priority: optional Homepage: http://www.biojava.org Description: Java API to biological data and applications (version 3) This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. . BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit. chroot-autobuild/build/buildd/libbiojava3-java_3.0.7+dfsg-1_all.deb: new debian package, version 2.0. size 2576 bytes: control archive= 956 bytes. 1276 bytes, 28 lines control 75 bytes, 1 lines md5sums Package: libbiojava3-java Source: biojava3-live Version: 3.0.7+dfsg-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 29 Depends: libbiojava3.0-java Provides: libbiojava3-java Section: java Priority: optional Homepage: http://www.biojava.org Description: Java API to biological data and applications (default version) BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit. . BioJava is provided by a vibrant community which meets annually at the Bioinformatics Open Source Conference (BOSC) that traditionally accompanies the Intelligent Systems in Molecular Biology (ISMB) meeting. Much like BioPerl, the employment of this library is valuable for everybody active in the field because of the many tricks of the trade one learns just by communicating on the mailing list. . This is a wrapper package which should enable smooth upgrades to new versions. chroot-autobuild/build/buildd/libbiojava3-java-doc_3.0.7+dfsg-1_all.deb: new debian package, version 2.0. size 1185426 bytes: control archive= 44957 bytes. 714 bytes, 18 lines control 185696 bytes, 1530 lines md5sums Package: libbiojava3-java-doc Source: biojava3-live Version: 3.0.7+dfsg-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 29167 Recommends: konqueror | html-browser Suggests: libbiojava3-java-demos, libbiojava3-java Section: doc Priority: optional Homepage: http://www.biojava.org Description: [Biology] Documentation for BioJava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. . This package contains the HTML documentation describing the API of BioJava which was generated automatically by JavaDoc. chroot-autobuild/build/buildd/libbiojava3.0-java_3.0.7+dfsg-1_all.deb: drwxr-xr-x root/root 0 2014-02-03 17:14 ./ drwxr-xr-x root/root 0 2014-02-03 17:14 ./usr/ drwxr-xr-x root/root 0 2014-02-03 17:14 ./usr/share/ drwxr-xr-x root/root 0 2014-02-03 17:14 ./usr/share/java/ -rw-r--r-- root/root 74001 2014-02-03 17:14 ./usr/share/java/biojava3-aa-prop-3.0.7.jar -rw-r--r-- root/root 57597 2014-02-03 17:14 ./usr/share/java/biojava3-phylo-3.0.7.jar -rw-r--r-- root/root 278965 2014-02-03 17:14 ./usr/share/java/biojava3-core-3.0.7.jar -rw-r--r-- root/root 249027 2014-02-03 17:14 ./usr/share/java/biojava3-protein-disorder-3.0.7.jar -rw-r--r-- root/root 61297 2014-02-03 17:14 ./usr/share/java/biojava3-genome-3.0.7.jar -rw-r--r-- root/root 1014382 2014-02-03 17:14 ./usr/share/java/biojava3-structure-3.0.7.jar -rw-r--r-- root/root 314894 2014-02-03 17:14 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./usr/share/doc/libbiojava3-java/api/org/biojava/bio/structure/Calc.html biojava3-live_3.0.7+dfsg-1_i386.changes: Format: 1.8 Date: Tue, 18 Jun 2013 14:40:39 +0200 Source: biojava3-live Binary: libbiojava3.0-java libbiojava3-java libbiojava3-java-doc Architecture: all Version: 3.0.7+dfsg-1 Distribution: trusty-proposed Urgency: low Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Olivier Sallou Description: libbiojava3-java - Java API to biological data and applications (default version) libbiojava3-java-doc - [Biology] Documentation for BioJava libbiojava3.0-java - Java API to biological data and applications (version 3) Changes: biojava3-live (3.0.7+dfsg-1) unstable; urgency=low . * New upstream release * Use Standards 3.9.5 . [debian/watch]: use new upstream GitHub repository Checksums-Sha1: 5bd5f0b416ebb13e67d441ca580db67dfe0d1581 3574170 libbiojava3.0-java_3.0.7+dfsg-1_all.deb 7a116eb5a0a88d85a7fed99b21a366e05dfce616 2576 libbiojava3-java_3.0.7+dfsg-1_all.deb e2280c2073c4ca7313272ad4e610298ab532a5ee 1185426 libbiojava3-java-doc_3.0.7+dfsg-1_all.deb Checksums-Sha256: a15a0828e21493f15240ebb63d8d4eae3d6b7195e30a899f6c18870e1200ea6f 3574170 libbiojava3.0-java_3.0.7+dfsg-1_all.deb b78ae9641328357faf3571b81b6ccce5029c5587c38da620eb7fcb6a30781759 2576 libbiojava3-java_3.0.7+dfsg-1_all.deb 09d97bb792fd53dbf837547be5717fa0e941e3fe1d4bb12c7c97f6f14f12bb5f 1185426 libbiojava3-java-doc_3.0.7+dfsg-1_all.deb Files: 5ee418f55f8cb71a41f98a73dbef1f4d 3574170 java optional libbiojava3.0-java_3.0.7+dfsg-1_all.deb 61442d42eee099ffa8fed3861d070896 2576 java optional libbiojava3-java_3.0.7+dfsg-1_all.deb f3f5310759407af226c5bb8f06ca5ce4 1185426 doc optional libbiojava3-java-doc_3.0.7+dfsg-1_all.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20140203-1715 Build needed 00:01:57, 131544k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5549150'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5549150/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5549150'] Unmounting chroot for build PACKAGEBUILD-5549150... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5549150'] Removing build PACKAGEBUILD-5549150