debian/0000755000000000000000000000000011771627607007204 5ustar debian/libpal-java-doc.install0000644000000000000000000000004111710536252013500 0ustar doc/* usr/share/doc/libpal-java debian/source/0000755000000000000000000000000011414066126010467 5ustar debian/source/format0000644000000000000000000000001411414066126011675 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000261211710530031011111 0ustar Format: http://dep.debian.net/deps/dep5/ Upstream-Name: PAL (Phylogenetic Analysis Library) Upstream-Contact: Matthew Goode Source: http://www.cebl.auckland.ac.nz/pal-project/ Files: * Copyright: © 2002-2011 Matthew Goode © 2000-2011 Alexei Drummond © 2001-2011 Ed Buckler © 1999-2011 Korbinian Strimmer License: LGPL-2.1 This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 2.1 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this program. If not, see . Comment: On Debian systems, you can read the full text of the GNU Lesser General Public License in ‘/usr/share/common-licenses/LGPL-2.1’. Files: debian/* Copyright: © 2012 Andreas Tille License: LGPL-2.1 Same License as the software itself. debian/rules0000755000000000000000000000051611771627015010257 0ustar #!/usr/bin/make -f JAVA_HOME=/usr/lib/jvm/default-java %: dh $@ --with javahelper override_dh_auto_clean: cd src; ant clean override_dh_auto_build: ant -buildfile src/build.xml -propertyfile debian/ant.properties ant -buildfile src/build.xml -propertyfile debian/ant.properties doc get-orig-source: . debian/get-orig-source debian/get-orig-source0000755000000000000000000000164311710516513012133 0ustar #!/bin/sh # unpack libpal-java tarball to get rid of several binaries set -e NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` UPSTREAMNAME=`echo $NAME | sed 's/lib\(.*\)-java/\1/'` if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` else VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${UPSTREAMNAME}.*?\1?"` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi TARDIR=pal-1.5.1 mkdir -p ../tarballs/${TARDIR} cd ../tarballs mv ../${TARDIR}-src.zip . cd ${TARDIR} unzip -q ../${TARDIR}-src.zip # Remove code which is not needed rm -rf src/org doc/COPYRIGHT-org.w3c.dom.html doc/.*html* cd .. GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -czf "$NAME"_"$VERSION".orig.tar.gz "${TARDIR}" rm -rf ${TARDIR} debian/libpal-java.jlibs0000644000000000000000000000001711710532204012366 0ustar src/dist/lib/* debian/watch0000644000000000000000000000017711710516326010226 0ustar version=3 http://www.cebl.auckland.ac.nz/pal-project/download.html bin/pal-([.\d]+)-src\.zip \ debian debian/get-orig-source debian/ant.properties0000644000000000000000000000017711771627015012102 0ustar # Ensure that source and target are 1.5 # For backwards compat on Java 7 ant.build.javac.source=1.5 ant.build.javac.target=1.5 debian/changelog0000644000000000000000000000076411771627255011064 0ustar libpal-java (1.5.1-2) unstable; urgency=low * Fix FTBFS with Java7 as default-java (thanks to Miguel Landaeta for the patch) Closes: #678562 * Bump Standards-Version to 3.9.3. No changes were required. * debhelper 9 (control+compat) -- Andreas Tille Sun, 24 Jun 2012 17:13:04 +0200 libpal-java (1.5.1-1) unstable; urgency=low * Initial Debian Upload (Closes: #657633) -- Andreas Tille Fri, 27 Jan 2012 13:57:54 +0100 debian/libpal-java-doc.javadoc0000644000000000000000000000005311710536572013451 0ustar src/dist/doc/api usr/share/doc/libpal-java debian/compat0000644000000000000000000000000211771627160010374 0ustar 9 debian/control0000644000000000000000000000331011771627171010600 0ustar Source: libpal-java Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille Build-Depends: debhelper (>= 9), javahelper (>=0.25) Build-Depends-Indep: default-jdk, ant Standards-Version: 3.9.3 Section: java Homepage: http://www.cebl.auckland.ac.nz/pal-project/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libpal-java/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/libpal-java/trunk/ Package: libpal-java Architecture: all Depends: ${java:Depends}, ${misc:Depends} Recommends: ${java:Recommends} Description: Phylogenetic Analysis Library The PAL project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. At present PAL consists of approximately 200 public classes/interfaces in 16 packages Please refer to the API documentation for a detailed description of all classes and methods available, and to the release history for an overview of the development history of PAL. Package: libpal-java-doc Architecture: all Section: doc Depends: ${java:Depends}, ${misc:Depends} Recommends: ${java:Recommends} Description: Phylogenetic Analysis Library - documentation The PAL project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. At present PAL consists of approximately 200 public classes/interfaces in 16 packages Please refer to the API documentation for a detailed description of all classes and methods available, and to the release history for an overview of the development history of PAL. . This package contains the documentation.