[med-svn] [grabix] 04/14: 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.
Andreas Tille
tille at debian.org
Fri Dec 8 20:09:52 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to annotated tag upstream/4.1
in repository grabix.
commit 05268885cca4346e41cc70ef4c8eda1f5d0311bc
Author: Steffen Moeller <moeller at debian.org>
Date: Thu Oct 4 23:21:42 2007 +0000
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
---
bla.txt | 24 --------
build.xml | 139 -----------------------------------------------
debian/README.Debian | 10 ++--
debian/changelog | 4 +-
debian/control | 6 +-
debian/patches/build.xml | 60 ++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 9 ++-
debian/watch | 10 +---
9 files changed, 77 insertions(+), 186 deletions(-)
diff --git a/bla.txt b/bla.txt
deleted file mode 100644
index 6f78552..0000000
--- a/bla.txt
+++ /dev/null
@@ -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
diff --git a/build.xml b/build.xml
deleted file mode 100644
index c7cd088..0000000
--- a/build.xml
+++ /dev/null
@@ -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>
diff --git a/debian/README.Debian b/debian/README.Debian
index ae9b0f7..8081a8d 100644
--- a/debian/README.Debian
+++ b/debian/README.Debian
@@ -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
diff --git a/debian/changelog b/debian/changelog
index 224d553..b58b7c2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -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
diff --git a/debian/control b/debian/control
index 2494438..db5519d 100644
--- a/debian/control
+++ b/debian/control
@@ -2,17 +2,17 @@ Source: haploview
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}, ${misc:Depends}
Description: Analysis and visualization of LD and haplotype maps
This tools assists �n the analysis of the nucleotide
variation in a population. Such investigations are performed
to determine genes and genetic pathways that are associated
with diseases. This is an early stage in the quest for new drugs.
.
- Homepage: http://www.broad.mit.edu/mpg/haploview/
diff --git a/debian/patches/build.xml b/debian/patches/build.xml
new file mode 100644
index 0000000..3823abb
--- /dev/null
+++ b/debian/patches/build.xml
@@ -0,0 +1,60 @@
+Index: haploview-4.0/build.xml
+===================================================================
+--- haploview-4.0.orig/build.xml 2007-10-05 00:37:11.044728970 +0200
++++ haploview-4.0/build.xml 2007-10-05 01:18:27.383231681 +0200
+@@ -14,6 +14,14 @@
+ <!-- Classpath -->
+
+ <path id="library.classpath">
++ <fileset dir="/usr/share/java/">
++ <include name="jfreechart.jar" />
++ <include name="log4j-1.2.jar" />
++ <include name="jgrapht.jar" />
++ <include name="jh.jar" />
++ <include name="jcommon.jar" />
++ <include name="batik-all.jar" />
++ </fileset>
+ <fileset dir="resources/">
+ <include name="*.jar"/>
+ <include name="*.zip"/>
+@@ -51,7 +59,9 @@
+
+ <target name="compile-haploview" depends="prepare-compile">
+ <javac srcdir="${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"/>
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c14487c
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+build.xml
diff --git a/debian/rules b/debian/rules
index da3a22b..fcf64fe 100755
--- a/debian/rules
+++ b/debian/rules
@@ -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 @@ DEB_ANT_INSTALL_TARGET=haploview
# 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/haploview::
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
diff --git a/debian/watch b/debian/watch
index 7af9880..4616eb8 100644
--- a/debian/watch
+++ b/debian/watch
@@ -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
-
-# Uncomment to find new files on sourceforge, for debscripts >= 2.9
-http://sf.net/haploview/Haploview(.*)\.tar\.gz
+http://sf.net/haploview/Haploview([0-9].*)\.tar\.gz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/grabix.git
More information about the debian-med-commit
mailing list