[Jpackage-commits] rpms/free/joone joone-2.0.0.pom, NONE, 1.1 joone-JooneGroovyScript.patch, NONE, 1.1 joone-TimeSeriesDemo1.patch, NONE, 1.1 joone-build.patch, NONE, 1.1 joone-editor-2.0.0.pom, NONE, 1.1 joone-engine-2.0.0.pom, NONE, 1.1 joone.spec, NONE, 1.1 joone_oat-ANOVATest.patch, NONE, 1.1 joone_oat-KruskalWallisTest.patch, NONE, 1.1 joone_oat-MannWhitneyUTest.patch, NONE, 1.1 joone_oat-RunStatisticSummary.patch, NONE, 1.1 joone_oat-StudentTTest.patch, NONE, 1.1 joone_oat-build.xml, NONE, 1.1 joone_oat-manifest.mf, NONE, 1.1

jpackage jpackage at ryu.zarb.org
Mon Jun 28 09:23:45 CEST 2010


Update of /home/projects/jpackage/cvs/rpms/free/joone
In directory ryu.zarb.org:/tmp/B5RHfOMj8D/rpms/free/joone

Added Files:
	joone-2.0.0.pom joone-JooneGroovyScript.patch 
	joone-TimeSeriesDemo1.patch joone-build.patch 
	joone-editor-2.0.0.pom joone-engine-2.0.0.pom joone.spec 
	joone_oat-ANOVATest.patch joone_oat-KruskalWallisTest.patch 
	joone_oat-MannWhitneyUTest.patch 
	joone_oat-RunStatisticSummary.patch 
	joone_oat-StudentTTest.patch joone_oat-build.xml 
	joone_oat-manifest.mf 
Log Message:
2.0.0-0.rc2.1.jpp6

--- NEW FILE: joone_oat-StudentTTest.patch ---
--- joone_oat/src/com/oat/experimenter/stats/analysis/twopopulation/StudentTTest.java.sav	2010-06-04 16:05:21.931100996 +0200
+++ joone_oat/src/com/oat/experimenter/stats/analysis/twopopulation/StudentTTest.java	2010-06-04 16:08:26.872394114 +0200
@@ -122,13 +122,13 @@
 	public void evaluate(double [] s1, double [] s2)
 		throws AnalysisException
 	{
-		DescriptiveStatistics ds1 = DescriptiveStatistics.newInstance();
+		DescriptiveStatistics ds1 = new DescriptiveStatistics();
         for (int i = 0; i < s1.length; i++)
         {
         	ds1.addValue(s1[i]);
         }
         
-		DescriptiveStatistics ds2 = DescriptiveStatistics.newInstance();
+		DescriptiveStatistics ds2 = new DescriptiveStatistics();
         for (int i = 0; i < s2.length; i++)
         {
         	ds2.addValue(s2[i]);

--- NEW FILE: joone_oat-MannWhitneyUTest.patch ---
--- joone_oat/src/com/oat/experimenter/stats/analysis/twopopulation/MannWhitneyUTest.java.math	2010-06-04 16:13:52.059634479 +0200
+++ joone_oat/src/com/oat/experimenter/stats/analysis/twopopulation/MannWhitneyUTest.java	2010-06-04 16:14:46.470838070 +0200
@@ -179,16 +179,7 @@
         // Z-Score
         zScore = result.getZScore();
         // P-value that populations are equal
-        String pValueTwoSided = result.getPValueTwoSided();
-        try
-        {
-        	pValue = Double.parseDouble(pValueTwoSided);
-        }
-        catch(NumberFormatException e)
-        {
-        	// I believe it means the pValue is too small to calculate, assume zero
-        	pValue = 0;
-        }
+        pValue = result.getPValueTwoSided();
         
         // U_STAT_EXPECTATION_FORMULA
         expectationFormula = result.getUMeanFormula();

--- NEW FILE: joone_oat-KruskalWallisTest.patch ---
--- joone_oat/src/com/oat/experimenter/stats/analysis/npopulation/KruskalWallisTest.java.math	2008-09-20 18:40:44.000000000 +0200
+++ joone_oat/src/com/oat/experimenter/stats/analysis/npopulation/KruskalWallisTest.java	2010-06-04 16:22:09.632352080 +0200
@@ -160,9 +160,9 @@
         }                
         // extract information
         degreesOfFreedom = Double.parseDouble(result.getDegreesOfFreedom());
-        tStatistic = Double.parseDouble(result.getTStat());
-        sSquared = Double.parseDouble(result.getSSqaured());
-        criticalValue = Double.parseDouble(result.getCriticalValue());             
+        tStatistic = result.getTStat();
+        sSquared = result.getSSqaured();
+        criticalValue = result.getCriticalValue();             
 
         // only do pair-wise sample comparisons if the NULL hypothesis can be rejected
         // The columns demonstrate the differences between the populations

--- NEW FILE: joone_oat-manifest.mf ---
Manifest-Version: 1.4
Main-Class: com.oat.gui.launcher.LauncherMain

--- NEW FILE: joone-2.0.0.pom ---
<project>
    <groupId>org.joone</groupId>
    <artifactId>joone</artifactId>
    <version>2.0.0</version>
  <modelVersion>4.0.0</modelVersion>
</project>

--- NEW FILE: joone-build.patch ---
--- build.xml.orig	2007-03-14 23:42:29.000000000 +0100
+++ build.xml	2010-06-04 16:53:29.840831636 +0200
@@ -76,20 +76,26 @@
 
 	<!-- classpath setting -->
 	<!--property name="junit.jar" value="${ext}/junit.jar"/-->
-	<property name="jhotdraw.jar" value="${ext}/jhotdraw.jar"/>
+	<property name="jhotdraw.jar" value="${ext}/jhotdraw5.jar"/>
 	<property name="log4j.jar" value="${ext}/log4j.jar"/>
-	<property name="jh.jar" value="${ext}/jh.jar"/>
-        <property name="poi-jars" value="${ext}/jakarta-poi.jar"/>
+	<property name="jh.jar" value="${ext}/javahelp2.jar"/>
+        <property name="poi-jars" value="${ext}/apache-poi.jar"/>
         <property name="bsh-jars" value="${ext}/bsh.jar"/>
         <property name="visad" value="${ext}/visad.jar"/>
-        <property name="groovy" value="${ext}/groovy.jar"/>
+        <property name="groovy" value="${ext}/groovy15.jar"/>
         <property name="xstream" value="${ext}/xstream.jar"/>
-        <property name="velocity" value="${ext}/velocity-dep.jar"/>
+        <property name="velocity" value="${ext}/velocity14.jar"/>
         <property name="property_sheet" value="${ext}/l2fprod-common-sheet.jar"/>
         <property name="nachocal" value="${ext}/nachocalendar.jar"/>
+        <property name="colt" value="${ext}/colt.jar"/>
+        <property name="jcommon" value="${ext}/jcommon.jar"/>
+        <property name="jfreechart" value="${ext}/jfreechart.jar"/>
+        <property name="oat" value="${ext}/oat.jar"/>
+        <property name="substance" value="${ext}/substance.jar"/>
         <property name="not_to_release" value="**/CVS/**"/>
 	<property name="classpath" value="${jhotdraw.jar};${poi-jars};${jh.jar};${bsh-jars};${visad}"/>
-        <property name="fullClasspath" value="${classpath};${log4j.jar};${groovy};${xstream};${velocity};${property_sheet};${nachocal}"/>
+        <property name="fullClasspath" 
+	value="${classpath};${log4j.jar};${groovy};${xstream};${velocity};${property_sheet};${nachocal};${colt};${jcommon};${jfreechart};${oat};${substance}"/>
   </target>
 
   <target name="fixforunix">
@@ -139,7 +145,7 @@
       <property name="excludes" value="${not_to_release},**/io/XLS*,**/*BeanInfo*,**/log/Log4J*,**/edit*/**,**/script*/*Script*,**/util/*Macro*"/>
       <!-- If we have java.beans.XMLEncoder in the path then we can save as XML -->    
       <echo message="Excluding: ${excludes}"/>
-      <javac classpath="${classpath}" debug="on" deprecation="yes" destdir="${lbuild}" excludes="${excludes}" includes="**/*.java" srcdir="${src}"> </javac>
+      <javac classpath="${fullClasspath}" debug="on" deprecation="yes" destdir="${lbuild}" excludes="${excludes}" includes="**/*.java" srcdir="${src}"> </javac>
   </target>
 
   <target depends="init" name="release">
@@ -226,6 +232,7 @@
         <zipfileset dir="${releases}" includes="SOMImageTester.jar" prefix="joone/lib"/>
         <zipfileset dir="${src}/org/joone" includes="samples/editor/**/*.*" prefix="joone"/>
         <zipfileset dir="${src}/org/joone/data" includes="layers.*" prefix="joone"/>
+<!--
         <zipfileset dir="${releases}/engine" includes="engine_release_changes.txt" prefix="joone"/>
         <zipfileset dir="${releases}/editor" includes="editor_release_changes.txt" prefix="joone"/>
         <zipfileset dir="${releases}/editor" includes="Readme.txt" prefix="joone"/>
@@ -233,6 +240,7 @@
         <zipfileset dir="${releases}/editor" includes="RunEditor.bat" prefix="joone"/>
         <zipfileset dir="${releases}/editor" filemode="755" includes="RunEditor.sh" prefix="joone"/>
         <zipfileset dir="${base}" excludes="**/crimson.jar,**/xalan.jar" includes="${joone_ext_lib}"/>
+-->
     </zip>
     
     <!-- Extensions -->

--- NEW FILE: joone-editor-2.0.0.pom ---
<project>
  <parent>
    <groupId>org.joone</groupId>
    <artifactId>joone</artifactId>
    <version>2.0.0</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>joone-editor</artifactId>
  <dependencies>
    <dependency>
      <groupId>org.joone</groupId>
      <artifactId>joone-engine</artifactId>
      <version>2.0.0</version>
    </dependency>
    <dependency>
      <groupId>org.jhotdraw</groupId>
      <artifactId>jhotdraw</artifactId>
      <version>5.2</version>
    </dependency>
    <dependency>
      <groupId>com.l2fprod.common</groupId>
      <artifactId>l2fprod-common-sheet</artifactId>
      <version>7.3</version>
    </dependency>
    <dependency>
      <groupId>com.thoughtworks.xstream</groupId>
      <artifactId>xstream</artifactId>
      <version>1.3.1</version>
    </dependency>
    <dependency>
      <groupId>visad</groupId>
      <artifactId>visad</artifactId>
      <version>2.0</version>
    </dependency>
  </dependencies>
</project>

--- NEW FILE: joone-JooneGroovyScript.patch ---
--- joone/org/joone/script/JooneGroovyScript.java.sav	2010-06-04 18:31:29.850766926 +0200
+++ joone/org/joone/script/JooneGroovyScript.java	2010-06-04 18:31:57.642359877 +0200
@@ -86,10 +86,10 @@
             log.error( "CompilationFailedException thrown. Message is : " + cfe.getMessage(),
             cfe);
         } 
-        catch (IOException ioe) {
-            log.error( "IOException thrown. Message is : " + ioe.getMessage(),
-            ioe);
-        }
+//      catch (IOException ioe) {
+//          log.error( "IOException thrown. Message is : " + ioe.getMessage(),
+//          ioe);
+//      }
     }
     
     public void set(String name, Object jObject){

--- NEW FILE: joone_oat-build.xml ---
<!-- 
Optimization Algorithm Toolkit (OAT)
http://sourceforge.net/projects/optalgtoolkit
Copyright (C) 2006, 2007  Jason Brownlee

OAT 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 3 of the License, or (at your option) any 
later version.

OAT 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 <http://www.gnu.org/licenses/>.

Jason Brownlee
Project Lead
OAT (Optimization Algorithm Toolkit)
http://sourceforge.net/projects/optalgtoolkit
-->

<!-- OAT Ant Build File -->

<project name="OAT" default="dist" basedir=".">
    <description>
        OAT ant build file
    </description>
  <!-- set global properties for this build -->
  <property name="src" location="src"/>
  <property name="lib" location="lib"/>
  <property name="build" location="build"/>
  <property name="dist"  location="dist"/>
  <property name="web"  location="web"/>
  <property name="ver"  value="1.4"/>
  <property name="OAT"  value="optalgtoolkit"/>

  <target name="init">
    <!-- Create the time stamp -->
    <tstamp/>

  </target>

  <target name="compile" depends="init"
        description="compile the source " >
    <!-- Create the build directory structure used by compile -->
    <mkdir dir="${build}"/>  	
    <!-- Compile the java code from ${src} into ${build} -->
    <javac srcdir="${src}" destdir="${build}">  	
	  	<!-- ensure libs are in the classpath  -->
	    <classpath>
	      <fileset dir="${lib}">
	        <include name="**/*.jar"/>
		    <include name="**/*.zip"/>	      	
	      </fileset>
	    </classpath>  	    	
    </javac>
    <copy todir="${build}" >
       <fileset dir="${src}">
       	  <include name="bcr/**"/>
       	  <include name="*.properties"/>
       	  <include name="META-INF/**"/>
       	  <include name="splash.jpg"/>
       </fileset>
    </copy>
  </target>

  <target name="dist" depends="compile"
        description="generate the distribution" >
    <!-- Create the distribution directory -->
    <mkdir dir="${dist}/DSTAMP"/>  	
    <!-- prepare the jar -->
    <jar jarfile="${dist}/DSTAMP/${OAT}.jar" basedir="${build}"
    	manifest="${build}/META-INF/MANIFEST.MF"/>
  	<!-- copy the libraries over -->
  	<mkdir dir="${dist}/DSTAMP/lib"/>
    <copy todir="${dist}/DSTAMP/lib" >
       <fileset dir="${lib}">
       	<include name="**/*.jar"/>
       	<include name="**/*.zip"/>       	
       </fileset>
    </copy>
  	<!-- copy the remaining release elements over -->
    <copy todir="${dist}/DSTAMP" >
       <fileset dir=".">
       	<include name="*.txt"/>
       </fileset>
    </copy>
  </target>
	
	
  <target name="release_download" depends="source"
        description="prepare the download release" >
    <!-- Create the distribution directory -->
    <mkdir dir="${dist}/DSTAMP-release_download"/>
    <!-- create the archive  -->
  	<zip destfile="${dist}/DSTAMP-release_download/${OAT}${ver}.zip" basedir="${dist}/DSTAMP"/>
  </target>
	
	
  <target name="release_web" depends="dist, javadoc"
        description="prepare web page content for deployment" >
    <!-- Create the distribution directory -->
    <mkdir dir="${dist}/DSTAMP-web"/>
  	<mkdir dir="${dist}/DSTAMP-web/applets"/>
  	<mkdir dir="${dist}/DSTAMP-web/applets/lib"/>
  	<mkdir dir="${dist}/DSTAMP-web/docs"/>
  	<mkdir dir="${dist}/DSTAMP-web/pics"/>
  	<mkdir dir="${dist}/DSTAMP-web/api"/>
  	<!-- copy everything we want over into the source directory -->
    <copy todir="${dist}/DSTAMP-web" >
       <fileset dir="${web}">
       	<include name="*.html"/>
       </fileset>  
    </copy>
    <copy todir="${dist}/DSTAMP-web/api" >
        <fileset dir="${dist}/DSTAMP-javadoc">
          <include name="**/*"/>
        </fileset>   
    </copy>
  	<copy todir="${dist}/DSTAMP-web/applets">
        <fileset dir="${web}/applets">
        	<include name="*.*"/>
        </fileset>  		
    </copy>    	  	
    <copy todir="${dist}/DSTAMP-web/applets/lib" >      
       <fileset dir="${lib}">
        <include name="**/*.jar"/>
        <include name="**/*.zip"/>       	
       </fileset>
       <fileset dir="${dist}/DSTAMP">
         <include name="${OAT}.jar"/>
       </fileset>    
    </copy>
  	
  	<copy todir="${dist}/DSTAMP-web/pics">
        <fileset dir="${web}/pics">
         <include name="*.*"/>
        </fileset>		
    </copy>  
  	<copy todir="${dist}/DSTAMP-web/docs">
        <fileset dir="${web}/docs">
         <include name="*.*"/>
        </fileset>  
    </copy> 
  	
  </target>	
	
	
	
  <target name="javadoc" depends="dist" description="Create OAT javadocs">
        <mkdir dir="${dist}/DSTAMP-javadoc" />
  	    <javadoc 
  	    	access="public" 
  	    	author="true" 
  	    	classpath="lib/jfreechart-1.0.2.jar;lib/junit-4.2.jar;lib/osp_core_v1.0.4.jar;lib/SOCR_plugin.jar;lib/ThirdPartyJars.jar;lib/colt.jar;lib/tsp.zip;lib/jcommon-1.0.5.jar;lib/SOCR_core.jar;lib/commons-math-1.1.jar;lib/ssj.jar;lib/gcp.zip" 
  	    	destdir="${dist}/DSTAMP-javadoc"
  	    	nodeprecated="false" 
  	    	nodeprecatedlist="false" 
  	    	noindex="false" 
  	    	nonavbar="false" 
  	    	notree="false" 
  	    	packagenames="com.oat.*" 
  	    	sourcepath="src" 
  	    	splitindex="false" 
  	    	use="false" 
  	    	version="true"/>  	
  </target>		
	
	
  <target name="source" depends="dist"
        description="prepare the source code for distribution, assuming it builds the dist ok" >
    <!-- Create the distribution directory -->
    <mkdir dir="${dist}/DSTAMP-source"/>
  	<!-- copy everything we want over into the source directory -->
    <copy todir="${dist}/DSTAMP-source" >
       <fileset dir=".">
       	<include name="src/**/*"/>
       	<include name="*.txt"/>
       	<include name="readme.txt"/>
       	<include name="build.xml"/>
       </fileset>
    </copy>
    <!-- create the archive  -->
  	<zip destfile="${dist}/DSTAMP/${OAT}${ver}-src.zip" 
  	     basedir="${dist}/DSTAMP-source"/>
  </target>	
	
	
  <target name="clean" depends="init"
        description="clean up" >
    <!-- Delete the ${build} and ${dist} directory trees -->
    <delete dir="${build}"/>
    <delete dir="${dist}"/>
  	<delete dir="${dist}/DSTAMP-source"/>
  	<delete dir="${dist}/DSTAMP-release_download"/>
  	<delete dir="${dist}/DSTAMP-web"/>
  	<delete dir="${dist}/DSTAMP-javadoc"/>
  </target>
	
</project>

--- NEW FILE: joone-engine-2.0.0.pom ---
<project>
  <parent>
    <groupId>org.joone</groupId>
    <artifactId>joone</artifactId>
    <version>2.0.0</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>joone-engine</artifactId>
  <dependencies>
    <dependency>
      <groupId>bsh</groupId>
      <artifactId>bsh</artifactId>
      <version>1.3.0</version>
    </dependency>
    <dependency>
      <groupId>colt</groupId>
      <artifactId>colt</artifactId>
      <version>1.2.0</version>
    </dependency>
    <dependency>
      <groupId>org.codehaus.groovy</groupId>
      <artifactId>groovy</artifactId>
      <version>1.5.6</version>
    </dependency>
    <dependency>
      <groupId>log4j</groupId>
      <artifactId>log4j</artifactId>
      <version>1.2.15</version>
    </dependency>
    <dependency>
      <groupId>org.apache.poi</groupId>
      <artifactId>poi</artifactId>
      <version>3.6</version>
    </dependency>
    <dependency>
      <groupId>velocity</groupId>
      <artifactId>velocity</artifactId>
      <version>1.4</version>
    </dependency>
    <dependency>
      <groupId>jfree</groupId>
      <artifactId>jfreechart</artifactId>
      <version>1.0.13</version>
    </dependency>
    <dependency>
      <groupId>jfree</groupId>
      <artifactId>jcommon</artifactId>
      <version>1.0.16</version>
    </dependency>
  </dependencies>
</project>

--- NEW FILE: joone-TimeSeriesDemo1.patch ---
--- joone/org/joone/samples/engine/timeseries/TimeSeriesDemo1.java.jfree	2008-09-18 13:56:14.000000000 +0200
+++ joone/org/joone/samples/engine/timeseries/TimeSeriesDemo1.java	2010-06-04 18:09:43.141894309 +0200
@@ -15,7 +15,7 @@
 import org.jfree.chart.ChartFactory;
 import org.jfree.chart.ChartPanel;
 import org.jfree.chart.JFreeChart;
-import org.jfree.chart.StandardLegend;
+//import org.jfree.chart.StandardLegend;
 import org.jfree.chart.axis.DateAxis;
 import org.jfree.chart.plot.XYPlot;
 import org.jfree.chart.renderer.xy.StandardXYItemRenderer;
@@ -26,7 +26,7 @@
 import org.jfree.data.xy.XYDataset;
 import org.jfree.ui.ApplicationFrame;
 import org.jfree.ui.RefineryUtilities;
-import org.jfree.ui.Spacer;
+//import org.jfree.ui.Spacer;
 
 /**
  * An example of a time series chart.  For the most part, default settings are used, except that
@@ -72,21 +72,21 @@
 
         chart.setBackgroundPaint(Color.white);
 
-        StandardLegend sl = (StandardLegend) chart.getLegend();
-        sl.setDisplaySeriesShapes(true);
+        //StandardLegend sl = (StandardLegend) chart.getLegend();
+        //sl.setDisplaySeriesShapes(true);
 
         XYPlot plot = chart.getXYPlot();
         plot.setBackgroundPaint(Color.lightGray);
         plot.setDomainGridlinePaint(Color.white);
         plot.setRangeGridlinePaint(Color.white);
-        plot.setAxisOffset(new Spacer(Spacer.ABSOLUTE, 5.0, 5.0, 5.0, 5.0));
+        //plot.setAxisOffset(new Spacer(Spacer.ABSOLUTE, 5.0, 5.0, 5.0, 5.0));
         plot.setDomainCrosshairVisible(true);
         plot.setRangeCrosshairVisible(true);
         
         XYItemRenderer renderer = plot.getRenderer();
         if (renderer instanceof StandardXYItemRenderer) {
             StandardXYItemRenderer rr = (StandardXYItemRenderer) renderer;
-            rr.setPlotShapes(true);
+            //rr.setPlotShapes(true);
             rr.setShapesFilled(true);
             rr.setItemLabelsVisible(true);
         }

--- NEW FILE: joone.spec ---
# Copyright (c) 2000-2010, JPackage Project
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
#    notice, this list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright
#    notice, this list of conditions and the following disclaimer in the
#    documentation and/or other materials provided with the
#    distribution.
# 3. Neither the name of the JPackage Project nor the names of its
#    contributors may be used to endorse or promote products derived
#    from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#

%define namedversion 2.0.0RC2

Name:           joone
Version:        2.0.0
Release:        0.rc2.1%{?dist}
Summary:        An Object Oriented Neural Engine

Group:          Development/Libraries
License:        LGPL
URL:            http://sourceforge.net/projects/joone/
Source0:        %{name}-%{namedversion}.tgz
# cvs -d:pserver:anonymous at joone.cvs.sourceforge.net:/cvsroot/joone login 
# cvs -z3 -d:pserver:anonymous at joone.cvs.sourceforge.net:/cvsroot/joone export -r HEAD joone
# tar czf ../SOURCES/joone-2.0.0RC2.tgz joone/

Source1:        %{name}-oat.tgz
# cvs -d:pserver:anonymous at joone.cvs.sourceforge.net:/cvsroot/joone login
# cvs -z3 -d:pserver:anonymous at joone.cvs.sourceforge.net:/cvsroot/joone co -P joone_oat
# tar czf ../SOURCES/joone-oat.tgz joone_oat/

Source2:        joone_oat-build.xml
Source3:        joone_oat-manifest.mf
Source4:        joone-%{version}.pom
Source5:        joone-editor-%{version}.pom
Source6:        joone-engine-%{version}.pom

Patch0:         joone-build.patch
Patch1:         joone_oat-StudentTTest.patch
Patch2:         joone_oat-KruskalWallisTest.patch
Patch3:         joone_oat-ANOVATest.patch
Patch4:         joone_oat-MannWhitneyUTest.patch
Patch5:         joone_oat-RunStatisticSummary.patch
Patch6:         joone-TimeSeriesDemo1.patch
Patch7:         joone-JooneGroovyScript.patch

BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)

BuildRequires:  jpackage-utils >= 0:5.0.0
BuildRequires:  java-devel >= 0:1.6
BuildRequires:  ant
BuildRequires:  apache-poi
BuildRequires:  axis
BuildRequires:  bsh
BuildRequires:  colt
BuildRequires:  groovy15
BuildRequires:  javahelp2
BuildRequires:  jcommon
BuildRequires:  jfreechart
BuildRequires:  jhotdraw5
BuildRequires:  l2fprod-common
BuildRequires:  log4j
BuildRequires:  nachocalendar
BuildRequires:  osp
BuildRequires:  socr
BuildRequires:  ssj
BuildRequires:  substance
BuildRequires:  velocity14
BuildRequires:  visad
BuildRequires:  xstream

Requires:  java >= 0:1.6
Requires:  apache-poi
Requires:  axis
Requires:  bsh
Requires:  colt
Requires:  groovy15
Requires:  javahelp2
Requires:  jcommon
Requires:  jfreechart
Requires:  jhotdraw5
Requires:  l2fprod-common
Requires:  log4j
Requires:  nachocalendar
Requires:  osp
Requires:  socr
Requires:  ssj
Requires:  substance
Requires:  velocity14
Requires:  visad
Requires:  xstream

BuildArch:      noarch
Requires(post):    jpackage-utils >= 0:5.0.0
Requires(postun):  jpackage-utils >= 0:5.0.0


%description
Joone is a neural net framework written in Java(tm). It's 
composed by a core engine, a GUI editor and a distributed 
training environment and can be extended by writing new 
modules to implement new algorithms or architectures starting 
from base component.


%package javadoc
Summary:        Javadoc documentation for %{name}
Group:          Documentation

%description javadoc
%{summary}.


%prep
%setup -q -n %{name}
gzip -dc %{SOURCE1} | tar xf -
cp %{SOURCE2} joone_oat/build.xml
mkdir -p joone_oat/src/META-INF/
cp %{SOURCE3} joone_oat/src/META-INF/MANIFEST.MF
for j in $(find . -name "*.jar"); do
    mv $j $j.no
done
ln -s $(build-classpath axis/axis) lib
ln -s $(build-classpath jhotdraw5) lib
ln -s $(build-classpath bsh) lib
ln -s $(build-classpath colt) lib
ln -s $(build-classpath groovy15) lib
ln -s $(build-classpath javahelp2) lib
ln -s $(build-classpath jcommon) lib
ln -s $(build-classpath jfreechart) lib
ln -s $(build-classpath l2fprod-common/l2fprod-common-sheet) lib
ln -s $(build-classpath nachocalendar) lib
#ln -s $(build-classpath oat) lib
ln -s $(build-classpath poi/apache-poi) lib
ln -s $(build-classpath velocity14) lib
ln -s $(build-classpath visad) lib
ln -s $(build-classpath xstream) lib
ln -s $(build-classpath log4j) lib
ln -s $(build-classpath osp) lib
ln -s $(build-classpath socr/SOCR_core) lib
ln -s $(build-classpath socr/SOCR_plugin) lib
ln -s $(build-classpath ssj) lib
ln -s $(build-classpath substance) lib

#1. Create a directory structure as the following:
#${base}
#   |___joone  (the source base dir - checkout here the CVS joone module)
#   |     |__org
#   |     |__lib
#   |___build  (the executable base dir - filled running the 'build' and 'rebuild' ANT targets)
#   |___doc    (the javadoc base dir - filled running the 'doc' ANT target)
mkdir joone
mv doc org lib joone
mkdir build
mkdir doc
mkdir releases
%patch0 -b .orig
%patch1 -b .math
%patch2 -b .math
%patch3 -b .math
%patch4 -b .math
%patch5 -b .math
%patch6 -b .jfree
%patch7 -b .groovy15


%build
pushd joone_oat
export CLASSPATH=$(build-classpath \
axis \
colt \
commons-math \
jcommon \
jfreechart \
junit4 \
osp \
socr/SOCR_core \
socr/SOCR_plugin \
ssj \
)
%{ant} -Dbuild.sysclasspath=first
popd
cp joone_oat/dist/DSTAMP/optalgtoolkit.jar joone/lib/oat.jar
%{ant} -Dbase=$(pwd) build lbuild doc release



%install
rm -rf $RPM_BUILD_ROOT
install -d $RPM_BUILD_ROOT%{_javadir} \
        $RPM_BUILD_ROOT%{_docdir}/%{name}-%{version} \
        $RPM_BUILD_ROOT%{_javadocdir}/%{name}-%{version}
install -m 644 releases/%{name}-engine.jar $RPM_BUILD_ROOT%{_javadir}/%{name}-engine-%{version}.jar
install -m 644 releases/%{name}-editor.jar $RPM_BUILD_ROOT%{_javadir}/%{name}-editor-%{version}.jar
ln -s %{name}-engine-%{version}.jar $RPM_BUILD_ROOT%{_javadir}/%{name}-engine.jar
ln -s %{name}-editor-%{version}.jar $RPM_BUILD_ROOT%{_javadir}/%{name}-editor.jar

cp -pr doc/api/* $RPM_BUILD_ROOT%{_javadocdir}/%{name}-%{version}

install -d -m 755 $RPM_BUILD_ROOT%{_datadir}/maven2/poms
install -m 644 %{SOURCE4} $RPM_BUILD_ROOT%{_datadir}/maven2/poms/JPP-%{name}.pom
%add_to_maven_depmap org.joone joone %{version} JPP %{name}
install -m 644 %{SOURCE5} $RPM_BUILD_ROOT%{_datadir}/maven2/poms/JPP-%{name}-editor.pom
%add_to_maven_depmap org.joone joone-editor %{version} JPP %{name}-editor
install -m 644 %{SOURCE6} $RPM_BUILD_ROOT%{_datadir}/maven2/poms/JPP-%{name}-engine.pom
%add_to_maven_depmap org.joone joone-engine %{version} JPP %{name}-engine

install -m 644 joone/doc/Latex_Doc/JooneCompleteGuide.pdf $RPM_BUILD_ROOT%{_docdir}/%{name}-%{version}

%clean
rm -rf $RPM_BUILD_ROOT

%post
%update_maven_depmap

%postun
%update_maven_depmap

%files
%defattr(-,root,root)
%{_javadir}/%{name}*.jar
%{_datadir}/maven2/poms/*
%{_mavendepmapfragdir}/*
%doc %{_docdir}/%{name}-%{version}

%files javadoc
%defattr(-,root,root)
%{_javadocdir}/%{name}-%{version}

%changelog
* Sat Jun 26 2010 Ralph Apel <r.apel at r-apel.de> - 2.0.0-0.rc2.1
- First release

--- NEW FILE: joone_oat-RunStatisticSummary.patch ---
--- joone_oat/src/com/oat/experimenter/stats/RunStatisticSummary.java.math	2010-06-04 16:16:05.361683037 +0200
+++ joone_oat/src/com/oat/experimenter/stats/RunStatisticSummary.java	2010-06-04 16:16:35.501242693 +0200
@@ -126,7 +126,7 @@
         
     	// summarize
     	numRecords = rawResults.length;
-    	descriptiveStatistics = DescriptiveStatistics.newInstance();
+    	descriptiveStatistics = new DescriptiveStatistics();
         for (int i = 0; i < rawResults.length; i++)
         {
         	descriptiveStatistics.addValue(rawResults[i]);

--- NEW FILE: joone_oat-ANOVATest.patch ---
--- joone_oat/src/com/oat/experimenter/stats/analysis/npopulation/ANOVATest.java.math	2010-06-04 16:12:04.893202998 +0200
+++ joone_oat/src/com/oat/experimenter/stats/analysis/npopulation/ANOVATest.java	2010-06-04 16:12:23.340933159 +0200
@@ -188,7 +188,7 @@
 		fValue = result.getFValue();
         try
         {
-            pValue = Double.parseDouble(result.getPValue()); 
+            pValue = result.getPValue(); 
         }
         catch(NumberFormatException nfe)
         {




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