[med-svn] r10992 - in trunk/forester/libforester-java/trunk: . debian debian/binary debian/patches debian/source
Olivier Sallou
osallou at alioth.debian.org
Thu May 24 13:08:47 UTC 2012
Author: osallou
Date: 2012-05-24 13:08:46 +0000 (Thu, 24 May 2012)
New Revision: 10992
Added:
trunk/forester/libforester-java/trunk/debian/
trunk/forester/libforester-java/trunk/debian/binary/
trunk/forester/libforester-java/trunk/debian/binary/forester
trunk/forester/libforester-java/trunk/debian/changelog
trunk/forester/libforester-java/trunk/debian/compat
trunk/forester/libforester-java/trunk/debian/control
trunk/forester/libforester-java/trunk/debian/copyright
trunk/forester/libforester-java/trunk/debian/docs
trunk/forester/libforester-java/trunk/debian/forester.install
trunk/forester/libforester-java/trunk/debian/get-orig-source.sh
trunk/forester/libforester-java/trunk/debian/libforester-java-doc.doc-base
trunk/forester/libforester-java/trunk/debian/libforester-java-doc.install
trunk/forester/libforester-java/trunk/debian/libforester-java.jlibs
trunk/forester/libforester-java/trunk/debian/patches/
trunk/forester/libforester-java/trunk/debian/patches/change_itext_packagename.patch
trunk/forester/libforester-java/trunk/debian/patches/fix_jar_path.patch
trunk/forester/libforester-java/trunk/debian/patches/series
trunk/forester/libforester-java/trunk/debian/rules
trunk/forester/libforester-java/trunk/debian/source/
trunk/forester/libforester-java/trunk/debian/source/format
Log:
[svn-inject] Applying Debian modifications (0.971-1) to trunk
Property changes on: trunk/forester/libforester-java/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/forester/libforester-java/trunk/debian/binary/forester
===================================================================
--- trunk/forester/libforester-java/trunk/debian/binary/forester (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/binary/forester 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+java -jar /usr/share/java/forester.jar
Property changes on: trunk/forester/libforester-java/trunk/debian/binary/forester
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/forester/libforester-java/trunk/debian/changelog
===================================================================
--- trunk/forester/libforester-java/trunk/debian/changelog (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/changelog 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,7 @@
+libforester-java (0.971-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #674269)
+ * Wait to know which revision in SVN we should take
+ * Ask upstream to put jars with version
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 24 May 2012 12:28:55 +0200
Added: trunk/forester/libforester-java/trunk/debian/compat
===================================================================
--- trunk/forester/libforester-java/trunk/debian/compat (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/compat 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1 @@
+8
Added: trunk/forester/libforester-java/trunk/debian/control
===================================================================
--- trunk/forester/libforester-java/trunk/debian/control (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/control 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,39 @@
+Source: libforester-java
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends: debhelper (>= 8.0.0),
+ default-jdk, junit4, javahelper (>=0.25), libcommons-codec, libitext-java
+Standards-Version: 3.9.3
+Homepage: http://code.google.com/p/forester
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/forester/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/forester/trunk/
+
+Package: forester
+Architecture: all
+Depends: ${misc:Depends}, libforester-java
+Description: Graphical vizualiation tool Archaeopteryx
+ Archaeopteryx is a software tool for the visualization, analysis,
+ and editing of potentially large and highly annotated phylogenetic trees.
+ It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and
+ as a standalone application.
+
+Package: libforester-java
+Architecture: all
+Depends: ${misc:Depends},
+ libcommons-codec, libitext-java
+Description: Libraries for evolutionary biology and comparative genomics research
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. It can be used to read or
+ write phylogenetic trees, export trees to graphics file,...
+
+Package: libforester-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Description: [Biology] Documentation for forester
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. This package contains the
+ JavaDoc documentation.
Added: trunk/forester/libforester-java/trunk/debian/copyright
===================================================================
--- trunk/forester/libforester-java/trunk/debian/copyright (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/copyright 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,44 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: forester
+Source: http://code.google.com/p/forester
+
+Files: *
+Copyright: 2010 Christian M. Zmasek
+ 2010 Sanford-Burnham Medical Research Institute
+License: LGPL 2.1+
+ This library 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 library 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 library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package 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 General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Added: trunk/forester/libforester-java/trunk/debian/docs
===================================================================
Added: trunk/forester/libforester-java/trunk/debian/forester.install
===================================================================
--- trunk/forester/libforester-java/trunk/debian/forester.install (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/forester.install 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1 @@
+debian/binary/forester usr/bin
Added: trunk/forester/libforester-java/trunk/debian/get-orig-source.sh
===================================================================
--- trunk/forester/libforester-java/trunk/debian/get-orig-source.sh (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/get-orig-source.sh 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d "-" -f1`
+version=$VERSION.svn.`date +"%Y%m%d"|tr -d '\n'`
+targetdir=libforester-java-$version
+origtargz=libforester-java_$VERSION.orig.tar.gz
+cd ..
+mkdir $targetdir
+svn checkout http://forester.googlecode.com/svn/forester/java $targetdir/java
+svn checkout http://forester.googlecode.com/svn/forester/resources $targetdir/resources
+find $targetdir -name ".svn" | xargs -r rm -r
+find $targetdir -name "*.jar" | xargs -r rm -r
+tar czf $origtargz $targetdir
+rm -rf $targetdir
+
Property changes on: trunk/forester/libforester-java/trunk/debian/get-orig-source.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/forester/libforester-java/trunk/debian/libforester-java-doc.doc-base
===================================================================
--- trunk/forester/libforester-java/trunk/debian/libforester-java-doc.doc-base (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/libforester-java-doc.doc-base 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,12 @@
+Document: forester
+Title: forester API
+Author: Forester developers
+Abstract: Javadoc-generated API for the forester library.
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. It can be used to read or
+ write phylogenetic trees, export trees to graphics file,...
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/libforester-java/api/index.html
+Files: /usr/share/doc/libforester-java/api/*.html /usr/share/doc/libforester-java/api/*/*/*/*.html /usr/share/doc/libforester-java/api/*/*/*/*/*.html /usr/share/doc/libforester-java/api/*/*/*/*/*/*.html
Added: trunk/forester/libforester-java/trunk/debian/libforester-java-doc.install
===================================================================
--- trunk/forester/libforester-java/trunk/debian/libforester-java-doc.install (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/libforester-java-doc.install 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1 @@
+doc/* /usr/share/doc/libforester-java/api/
Added: trunk/forester/libforester-java/trunk/debian/libforester-java.jlibs
===================================================================
--- trunk/forester/libforester-java/trunk/debian/libforester-java.jlibs (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/libforester-java.jlibs 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1 @@
+java/forester.jar
Added: trunk/forester/libforester-java/trunk/debian/patches/change_itext_packagename.patch
===================================================================
--- trunk/forester/libforester-java/trunk/debian/patches/change_itext_packagename.patch (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/patches/change_itext_packagename.patch 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,29 @@
+Author: Olivier Sallou <osallou at debian.org>
+Subject: change package name for itext
+Description: Upstream refers to com.itext hwile Debian package
+ itext use package name com.lowagie. Replace in the file the package
+ name references
+Last-Updated: 24/05/12
+--- a/java/src/org/forester/archaeopteryx/PdfExporter.java
++++ b/java/src/org/forester/archaeopteryx/PdfExporter.java
+@@ -35,13 +35,13 @@
+
+ import org.forester.phylogeny.Phylogeny;
+
+-import com.itextpdf.text.Document;
+-import com.itextpdf.text.DocumentException;
+-import com.itextpdf.text.FontFactory;
+-import com.itextpdf.text.Rectangle;
+-import com.itextpdf.text.pdf.DefaultFontMapper;
+-import com.itextpdf.text.pdf.PdfContentByte;
+-import com.itextpdf.text.pdf.PdfWriter;
++import com.lowagie.text.Document;
++import com.lowagie.text.DocumentException;
++import com.lowagie.text.FontFactory;
++import com.lowagie.text.Rectangle;
++import com.lowagie.text.pdf.DefaultFontMapper;
++import com.lowagie.text.pdf.PdfContentByte;
++import com.lowagie.text.pdf.PdfWriter;
+
+ /*
+ *
Added: trunk/forester/libforester-java/trunk/debian/patches/fix_jar_path.patch
===================================================================
--- trunk/forester/libforester-java/trunk/debian/patches/fix_jar_path.patch (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/patches/fix_jar_path.patch 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,68 @@
+Author: Olivier Sallou <osallou at debian.org>
+Subject: Change dependency libraries path
+Description: Use Debian libraries instead of upstream
+ included ones
+Last-Updated: 24/05/12
+--- a/java/build.xml
++++ b/java/build.xml
+@@ -3,9 +3,9 @@
+
+ <property name="src.dir" value="src" />
+ <property name="classes.dir" value="classes" />
+- <property name="jars.dir" value="resources" />
+- <property name="itextjar" value="${jars.dir}/itextpdf-5.1.0.jar" />
+- <property name="commonscodecjar" value="${jars.dir}/commons-codec-1.5.jar" />
++ <property name="jars.dir" value="/usr/share/java" />
++ <property name="itextjar" value="${jars.dir}/itext.jar" />
++ <property name="commonscodecjar" value="${jars.dir}/commons-codec.jar" />
+ <property name="forester_jar" value="forester.jar" />
+ <property name="archaeopteryx_applets_jar" value="archaeopteryx_applets.jar" />
+
+@@ -40,34 +40,15 @@
+ </target>
+
+ <target name="jar" description="JARs the classes files" depends="compile,copy_resources">
+- <unjar src="${itextjar}" dest="${classes.dir}">
+- <patternset>
+- <include name="**/*.class" />
+- <include name="**/*.afm" />
+- <include name="**/*.txt" />
+- <exclude name="**/*Test*.class" />
+- </patternset>
+- </unjar>
+- <unjar src="${commonscodecjar}" dest="${classes.dir}">
+- <patternset>
+- <include name="**/*.class" />
+- <exclude name="**/*Test*.class" />
+- </patternset>
+- </unjar>
+ <jar level="9" destfile="${forester_jar}" basedir="${classes.dir}" excludes="**/Test.class" duplicate="fail" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="org.forester.archaeopteryx.Archaeopteryx" />
++ <attribute name="Class-Path" value="${itextjar};${commonscodecjar}"/>
+ </manifest>
+ </jar>
+ </target>
+
+ <target name="jar_applets_only" description="JARs the classes files" depends="compile_applets_only,copy_resources">
+- <unjar src="${commonscodecjar}" dest="${classes.dir}">
+- <patternset>
+- <include name="**/*.class" />
+- <exclude name="**/*Test*.class" />
+- </patternset>
+- </unjar>
+ <jar level="9" destfile="${archaeopteryx_applets_jar}" basedir="${classes.dir}" excludes="org/forester/application/**
+ org/forester/development/**
+ org/forester/evoinference/**
+@@ -87,4 +68,11 @@
+ <target name="applets_only" description="" depends="jar_applets_only">
+ </target>
+
++ <target name="javadoc">
++ <mkdir dir="../doc"/>
++ <javadoc destdir="../doc" sourcepath="${src.dir}" >
++ <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
++ </javadoc>
++ </target>
++
+ </project>
Added: trunk/forester/libforester-java/trunk/debian/patches/series
===================================================================
--- trunk/forester/libforester-java/trunk/debian/patches/series (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/patches/series 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,2 @@
+fix_jar_path.patch
+change_itext_packagename.patch
Added: trunk/forester/libforester-java/trunk/debian/rules
===================================================================
--- trunk/forester/libforester-java/trunk/debian/rules (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/rules 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1,19 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_build:
+ cd java && ant
+ cd java && ant javadoc
+
+override_dh_clean:
+ cd java && ant clean
+ rm -rf doc
+ dh_clean
+
+get-orig-source:
+ debian/get-orig-source.sh
Property changes on: trunk/forester/libforester-java/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/forester/libforester-java/trunk/debian/source/format
===================================================================
--- trunk/forester/libforester-java/trunk/debian/source/format (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/source/format 2012-05-24 13:08:46 UTC (rev 10992)
@@ -0,0 +1 @@
+3.0 (quilt)
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