[med-svn] r596 - in trunk/packages/haploview/trunk: . debian debian/patches
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Thu Oct 4 23:21:42 UTC 2007
Author: smoe-guest
Date: 2007-10-04 23:21:42 +0000 (Thu, 04 Oct 2007)
New Revision: 596
Added:
trunk/packages/haploview/trunk/debian/patches/
trunk/packages/haploview/trunk/debian/patches/build.xml
trunk/packages/haploview/trunk/debian/patches/series
Removed:
trunk/packages/haploview/trunk/bla.txt
trunk/packages/haploview/trunk/build.xml
Modified:
trunk/packages/haploview/trunk/debian/README.Debian
trunk/packages/haploview/trunk/debian/changelog
trunk/packages/haploview/trunk/debian/control
trunk/packages/haploview/trunk/debian/rules
trunk/packages/haploview/trunk/debian/watch
Log:
Haploview is a nice package to display genetic linkage disequilibria. Many geneticists and medical doctors alike love it. Some more would love it if they knew about it, but, well, this is part of what Debian is for.
For some mysterious reasons I do not get it to compile, something it once
did for version 3.3:
BUILD FAILED
/home/moeller/svn/debian-med/trunk/packages/haploview/build-area/haploview-4.0/build.xml:63: Unable to find a javac compiler;
com.sun.tools.javac.Main is not on the classpath.
Perhaps JAVA_HOME does not point to the JDK.
It is currently set to "/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre"
Total time: 1 second
make: *** [common-install-impl] Fehler 1
Command dpkg-buildpackage -us -uc -rfakeroot failed in <unknown>, how to continue now? [Qri?]:
If anyone could help out here, then I would very much appreciate it.
Cheers,
Steffen
Deleted: trunk/packages/haploview/trunk/bla.txt
===================================================================
--- trunk/packages/haploview/trunk/bla.txt 2007-10-04 22:16:50 UTC (rev 595)
+++ trunk/packages/haploview/trunk/bla.txt 2007-10-04 23:21:42 UTC (rev 596)
@@ -1,24 +0,0 @@
-dpkg-buildpackage: source package is haploview
-dpkg-buildpackage: source version is 3.3-1
-dpkg-buildpackage: source changed by Steffen Moeller <moeller at unknown>
-dpkg-buildpackage: host architecture i386
-dpkg-buildpackage: source version without epoch 3.3-1
-test -x debian/rules
-test "`id -u`" = 0
-dh_clean
-cd . && /usr/bin/java -classpath /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/lib/kaffe/lib/tools.jar -Dant.home=/usr/share/ant org.apache.tools.ant.Main -Dcompile.debug=true -Dcompile.optimize=true clean
-Buildfile: build.xml
-
-init:
-
-clean:
- [delete] Deleting directory /local/debian/home/moeller/debian/haploview/haploview-3.3/build
-
-BUILD SUCCESSFUL
-Total time: 0 seconds
-rm -f debian/stamp-ant-build
-dh_clean resources/jgrapht* Haploview.jar
-rm -rf build resources/jfreechart
-touch debian/files
-dpkg-source: building haploview using existing haploview_3.3.orig.tar.gz
-dpkg-source: building haploview in haploview_3.3-1.diff.gz
Deleted: trunk/packages/haploview/trunk/build.xml
===================================================================
--- trunk/packages/haploview/trunk/build.xml 2007-10-04 22:16:50 UTC (rev 595)
+++ trunk/packages/haploview/trunk/build.xml 2007-10-04 23:21:42 UTC (rev 596)
@@ -1,139 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- Initial Set-Up -->
-
-<project name="HaploView" default="main" basedir=".">
-
- <path id="haploview.root">
- <pathelement location="${basedir}"/>
- </path>
-
-
-
-<!-- Get all the files in the /resources directory and add them to the -->
-<!-- Classpath -->
-
- <path id="library.classpath">
- <fileset dir="/usr/share/java/">
- <include name="jgrapht.jar"/>
- <include name="jfreechart.jar"/>
- <include name="jcommon.jar"/>
- </fileset>
-<!--
- <fileset dir="resources/">
- <include name="*.jar"/>
- <include name="*.zip"/>
- </fileset>
--->
- <fileset dir="docs/">
- <include name="HaploHelp.jar"/>
- </fileset>
-</path>
-
- <!-- =========================================================== -->
- <!-- Initialization -->
- <!-- =========================================================== -->
-<!-- Setup project roots -->
- <target name="init">
- <property name="haploview.root" value="${basedir}"/>
- <property name="haploview.build" value="${haploview.root}/build"/>
- <property name="haploview.dist" value="${haploview.root}/dist"/>
- <property name="haploview.classes" value="${haploview.build}/classes"/>
- <property name="haploview.src" value="${haploview.root}"/>
- <property name="haploview.lib" value="${haploview.root}/resources"/>
- <property name="haploview.package" value="edu/mit/wi/"/>
- <tstamp>
- <format property="build.number" pattern="yyyyMMddHHmm"/>
- </tstamp>
-</target>
-
-<!-- Prepare src directory for compilation step -->
-
-<target name="prepare-compile" depends="init">
- <mkdir dir="${haploview.classes}"/>
-</target>
-
-<!-- Compile the Haploview application -->
-
-<target name="compile-haploview" depends="prepare-compile">
- <javac srcdir="${haploview.src}" destdir="${haploview.classes}"
- includes="${haploview.package}/**" debug="on">
- <classpath refid="library.classpath"/>
- </javac>
-
- <copy file="resources/orator.raw" todir="build/classes/edu/mit/wi/haploview/"/>
-</target>
-
-
-
-<!-- this target makes the jar with HVWrap as the main class, which -->
-<!-- uses automagic -Xmx stuff, and suppresses error output -->
-<target name = "haploview-release" depends="compile-haploview">
- <jar jarfile="Haploview.jar">
- <fileset dir="${haploview.classes}">
- <include name="edu/mit/wi/**/**"/>
- </fileset>
- <manifest>
- <attribute name="Built-By" value="${user.name}"/>
- <attribute name="Main-Class" value="edu.mit.wi.haploview.HVWrap"/>
- </manifest>
- <zipfileset src="resources/JimiProClasses.zip"/>
- <zipfileset src="resources/jh.jar"/>
- <zipfileset src="docs/HaploHelp.jar"/>
-<!--
- <zipfileset src="resources/jgrapht-0.5.3.jar"/>
--->
- <zipfileset src="/usr/share/java/jgrapht.jar"/>
-<!--
- <zipfileset src="resources/jfreechart/jfreechart-1.0.1.jar"/>
- <zipfileset src="resources/jfreechart/jcommon-1.0.0.jar"/>
--->
- <zipfileset src="/usr/share/java/jfreechart.jar"/>
- <zipfileset src="/usr/share/java/jcommon.jar"/>
- </jar>
-</target>
-
-
-<!-- Jar the application up -->
-<target name="haploview" depends="compile-haploview">
- <jar jarfile="Haploview.jar">
- <fileset dir="${haploview.classes}">
- <include name="edu/mit/wi/**/**"/>
- </fileset>
- <manifest>
- <attribute name="Built-By" value="${user.name}"/>
- <attribute name="Main-Class" value="edu.mit.wi.haploview.HaploView"/>
- </manifest>
- <zipfileset src="resources/JimiProClasses.zip"/>
- <zipfileset src="resources/jh.jar"/>
- <zipfileset src="docs/HaploHelp.jar"/>
-<!-- <zipfileset src="resources/jgrapht-0.5.3.jar"/> -->
- <zipfileset src="/usr/share/java/jgrapht.jar"/>
-<!--
- <zipfileset src="resources/jfreechart/jfreechart-1.0.1.jar"/>
- <zipfileset src="resources/jfreechart/jcommon-1.0.0.jar"/>
--->
- <zipfileset src="/usr/share/java/jfreechart.jar"/>
- <zipfileset src="/usr/share/java/jcommon.jar"/>
- </jar>
-</target>
-
-<target name="clean" depends="init">
- <delete dir="${haploview.build}"/>
-</target>
-
-<target name="main" depends="init">
- <echo message="------------------------------------------------------------"/>
- <echo message="welcome to haploview build file"/>
- <echo message="Usage: ant [target-name]"/>
- <echo message="where [target-name] is one of the following targets:"/>
- <echo message="compile-haploview --> compiles the haploview classes
- only"/>
- <echo message="haploview-release --> makes 'wrapped' jar with auto Xmx"/>
- <echo message="haploview --> makes the executable jar file"/>
- <echo message="clean --> cleans up after itself removing the build directory"/>
- <echo message="------------------------------------------------------------"/>
-</target>
-
-
-</project>
Modified: trunk/packages/haploview/trunk/debian/README.Debian
===================================================================
--- trunk/packages/haploview/trunk/debian/README.Debian 2007-10-04 22:16:50 UTC (rev 595)
+++ trunk/packages/haploview/trunk/debian/README.Debian 2007-10-04 23:21:42 UTC (rev 596)
@@ -1,10 +1,8 @@
haploview for Debian
--------------------
-Quite frustrating for me but possibly stimulating for others,
-this package builds with kaffe but does not run without the Sun JDK.
+javahelp2 has just appeared on Debian and thus
+the packaging of Haploview can continue. Many
+thanks for that!
-The watch file indicates the older 3.1.1 version rather than the 3.3
-since upstream omitted the second dot as a separator on sourceforge.net.
-
- -- Steffen Moeller <steffen_moeller at gmx.de> Sun, 14 Jan 2007 15:28:10 +0100
+ -- Steffen Moeller <moeller at debian.org> Sun, 14 Jan 2007 15:28:10 +0100
Modified: trunk/packages/haploview/trunk/debian/changelog
===================================================================
--- trunk/packages/haploview/trunk/debian/changelog 2007-10-04 22:16:50 UTC (rev 595)
+++ trunk/packages/haploview/trunk/debian/changelog 2007-10-04 23:21:42 UTC (rev 596)
@@ -1,6 +1,6 @@
-haploview (3.3-1) unstable; urgency=low
+haploview (4.0-1) unstable; urgency=low
* Initial release (Closes: #311421)
- -- Steffen Moeller <moeller at unknown> Sun, 14 Jan 2007 15:28:10 +0100
+ -- Steffen Moeller <moeller at debian.org> Sun, 14 Jan 2007 15:28:10 +0100
Modified: trunk/packages/haploview/trunk/debian/control
===================================================================
--- trunk/packages/haploview/trunk/debian/control 2007-10-04 22:16:50 UTC (rev 595)
+++ trunk/packages/haploview/trunk/debian/control 2007-10-04 23:21:42 UTC (rev 596)
@@ -2,17 +2,17 @@
Section: contrib/science
Priority: extra
Maintainer: Steffen Moeller <steffen_moeller at gmx.de>
-Build-Depends-Indep: cdbs, ant, debhelper (>= 5), kaffe|java-compiler,libjfreechart-java,libjgrapht-java
+Build-Depends-Indep: cdbs, ant, debhelper (>= 5), kaffe|java-compiler, libjfreechart-java, libjgrapht-java, liblog4j1.2-java, javahelp2
Standards-Version: 3.7.2
+Homepage: http://www.broad.mit.edu/mpg/haploview/
Package: haploview
Architecture: all
-Depends: java-virtual-machine, sun-java5-jre|java2-runtime,libjfreechart-java,libjgrapht-java, ${shlibs:Depends}, ${misc:Depends}
+Depends: java-virtual-machine, sun-java5-jre|java2-runtime,libjfreechart-java,libjgrapht-java, libjcommon-java, liblog4j1.2-java, javahelp2, libbatik-java, ${shlibs:Depends}, ${misc:Depends}
Description: Analysis and visualization of LD and haplotype maps
This tools assists ín the analysis of the nucleotide
variation in a population. Such investigations are performed
to determine genes and genetic pathways that are associated
with diseases. This is an early stage in the quest for new drugs.
.
- Homepage: http://www.broad.mit.edu/mpg/haploview/
Added: trunk/packages/haploview/trunk/debian/patches/build.xml
===================================================================
--- trunk/packages/haploview/trunk/debian/patches/build.xml (rev 0)
+++ trunk/packages/haploview/trunk/debian/patches/build.xml 2007-10-04 23:21:42 UTC (rev 596)
@@ -0,0 +1,60 @@
+Index: haploview-4.0/build.xml
+===================================================================
+--- haploview-4.0.orig/build.xml 2007-10-05 00:37:11.044728970 +0200
++++ haploview-4.0/build.xml 2007-10-05 01:18:27.383231681 +0200
+@@ -14,6 +14,14 @@
+ <!-- Classpath -->
+
+ <path id="library.classpath">
++ <fileset dir="/usr/share/java/">
++ <include name="jfreechart.jar" />
++ <include name="log4j-1.2.jar" />
++ <include name="jgrapht.jar" />
++ <include name="jh.jar" />
++ <include name="jcommon.jar" />
++ <include name="batik-all.jar" />
++ </fileset>
+ <fileset dir="resources/">
+ <include name="*.jar"/>
+ <include name="*.zip"/>
+@@ -51,7 +59,9 @@
+
+ <target name="compile-haploview" depends="prepare-compile">
+ <javac srcdir="${haploview.src}" destdir="${haploview.classes}"
+- includes="${haploview.package}/**" debug="on" target="1.4">
++ includes="${haploview.package}/**" debug="on"
++ >
++ <!-- target="1.4" -->
+ <classpath refid="library.classpath"/>
+ </javac>
+
+@@ -72,12 +82,16 @@
+ <attribute name="Main-Class" value="edu.mit.wi.haploview.HVWrap"/>
+ </manifest>
+ <zipfileset src="resources/JimiProClasses.zip"/>
++<!--
+ <zipfileset src="resources/jh.jar"/>
++-->
+ <zipfileset src="docs/HaploHelp.jar"/>
++<!--
+ <zipfileset src="resources/jgrapht-0.5.3.jar"/>
+ <zipfileset src="resources/log4j-1.2.14.jar"/>
+ <zipfileset src="resources/jfreechart/jfreechart-1.0.5.jar"/>
+ <zipfileset src="resources/jfreechart/jcommon-1.0.9.jar"/>
++-->
+ <zipfileset src="resources/jfreechart/batik-xml.jar"/>
+ <zipfileset src="resources/jfreechart/xml-apis.jar"/>
+ <zipfileset src="resources/jfreechart/batik-awt-util.jar"/>
+@@ -102,10 +116,12 @@
+ <zipfileset src="resources/JimiProClasses.zip"/>
+ <zipfileset src="resources/jh.jar"/>
+ <zipfileset src="docs/HaploHelp.jar"/>
++<!--
+ <zipfileset src="resources/jgrapht-0.5.3.jar"/>
+ <zipfileset src="resources/log4j-1.2.14.jar"/>
+ <zipfileset src="resources/jfreechart/jfreechart-1.0.5.jar"/>
+ <zipfileset src="resources/jfreechart/jcommon-1.0.9.jar"/>
++-->
+ <zipfileset src="resources/jfreechart/batik-xml.jar"/>
+ <zipfileset src="resources/jfreechart/xml-apis.jar"/>
+ <zipfileset src="resources/jfreechart/batik-awt-util.jar"/>
Added: trunk/packages/haploview/trunk/debian/patches/series
===================================================================
--- trunk/packages/haploview/trunk/debian/patches/series (rev 0)
+++ trunk/packages/haploview/trunk/debian/patches/series 2007-10-04 23:21:42 UTC (rev 596)
@@ -0,0 +1 @@
+build.xml
Modified: trunk/packages/haploview/trunk/debian/rules
===================================================================
--- trunk/packages/haploview/trunk/debian/rules 2007-10-04 22:16:50 UTC (rev 595)
+++ trunk/packages/haploview/trunk/debian/rules 2007-10-04 23:21:42 UTC (rev 596)
@@ -1,8 +1,12 @@
#!/usr/bin/make -f
+include /usr/share/quilt/quilt.make
+
include /usr/share/cdbs/1/rules/debhelper.mk
#include /usr/share/cdbs/1/class/makefile.mk
include /usr/share/cdbs/1/class/ant.mk
+#include /usr/share/quilt/quilt.make
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
JAVA_HOME=/usr/lib/kaffe
JAVACMD=/usr/bin/java
@@ -10,11 +14,10 @@
# Add here any variable or target overrides you need.
-DEB_JARS = jcommon,jgrapht,jfreechart
+DEB_JARS = jcommon,jgrapht,jfreechart,jh
DEB_INSTALL_EXAMPLES_haploview=$(shell ls examples/*)
-
common-install-impl:: install/haploview
#install/libjline-java-doc
@@ -23,7 +26,7 @@
install -p -m 644 -D Haploview.jar $(DEB_FINALDIR)/usr/share/haploview/Haploview.jar
install -p -m 755 -D haploview.sh $(DEB_FINALDIR)/usr/bin/haploview
-clean::
+clean:: unpatch
dh_clean resources/jgrapht* Haploview.jar
rm -rf build resources/jfreechart
touch debian/files
Modified: trunk/packages/haploview/trunk/debian/watch
===================================================================
--- trunk/packages/haploview/trunk/debian/watch 2007-10-04 22:16:50 UTC (rev 595)
+++ trunk/packages/haploview/trunk/debian/watch 2007-10-04 23:21:42 UTC (rev 596)
@@ -1,12 +1,4 @@
-# Example watch control file for uscan
-# Rename this file to "watch" and then you can run the "uscan" command
-# to check for upstream updates and more.
-# See uscan(1) for format
-
-# Compulsory line, this is a version 3 file
version=3
+http://sf.net/haploview/Haploview([0-9].*)\.tar\.gz
-# Uncomment to find new files on sourceforge, for debscripts >= 2.9
-http://sf.net/haploview/Haploview(.*)\.tar\.gz
-
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