[pkg-java] r13532 - in trunk/jalview/debian: . patches source
Vincent Fourmond
fourmond at alioth.debian.org
Thu Apr 14 22:29:54 UTC 2011
Author: fourmond
Date: 2011-04-14 22:29:53 +0000 (Thu, 14 Apr 2011)
New Revision: 13532
Added:
trunk/jalview/debian/javabuild
trunk/jalview/debian/source/
trunk/jalview/debian/source/format
Removed:
trunk/jalview/debian/patches/00list
trunk/jalview/debian/patches/10-build.dpatch
Modified:
trunk/jalview/debian/changelog
trunk/jalview/debian/control
trunk/jalview/debian/new-upstream
trunk/jalview/debian/rules
Log:
[jalview] Mutilation of my old packaging of jalview; there is still quite a lot of work to do...
Modified: trunk/jalview/debian/changelog
===================================================================
--- trunk/jalview/debian/changelog 2011-04-14 21:37:44 UTC (rev 13531)
+++ trunk/jalview/debian/changelog 2011-04-14 22:29:53 UTC (rev 13532)
@@ -1,24 +1,9 @@
-jalview (2.4.dfsg-1) UNRELEASED unstable; urgency=low
+jalview (2.6.1.dfsg-1) unstable; urgency=low
- * DO NOT UPLOAD THIS PACKAGE: WORK IN PROGRESS !
* Initial release (Closes: #507436)
* Adding a debian/new-upstream script to repackage the original
- tarball, getting rid of the non-free bits.
- * debian/patches/10-build.dpatch: disable features that depends
- on things removed from the .dfsg tarball
- * Dropping provided xercesImpl.jar, (build)?-dep on libxerces2-java
- * Dropping provided xml-apis.jar, (build)?-dep on libxalan2-java
- * Dropping provided axis.jar and saaj.jar, (build)?-dep on libaxis-java
- * Also dropping jaxrpc.jar, also in libaxis-java
- * Dropping provided log4j-1.2.8.jar, (build)?-dep on liblog4j1.2-java
- * Dropping provided jhall.jar, (build)?-dep on javahelp2
- * debian/patches/10-build.dpatch: tweaked the classpath of the
- buildindices task for it to find the class.
- * Dropping provided commons-discovery.jar, (build)?-dep on
- libcommons-discovery-java
- * Dropping provided commons-logging.jar, (build)?-dep on
- libcommons-logging-java
- * Dropping provided regex.jar, (build)?-dep on libstevesoft-regex-java
- * Dropping provided JMol.jar, now that jmol has been packaged for Debian !
+ tarball, getting rid of the bundled JAR file (I love JAR files)
+ * Using dh 7 and javahelper
+ * Using jh_build for building
- -- Vincent Fourmond <fourmond at debian.org> Thu, 14 Apr 2011 16:52:07 +0200
+ -- Vincent Fourmond <fourmond at debian.org> Fri, 15 Apr 2011 00:28:48 +0200
Modified: trunk/jalview/debian/control
===================================================================
--- trunk/jalview/debian/control 2011-04-14 21:37:44 UTC (rev 13531)
+++ trunk/jalview/debian/control 2011-04-14 22:29:53 UTC (rev 13532)
@@ -3,12 +3,14 @@
Priority: optional
Maintainer: Vincent Fourmond <fourmond at debian.org>
Build-Depends: cdbs, debhelper (>= 7), default-jdk,
- ant, ant-optional, dpatch, libxerces2-java, libxalan2-java,
+ ant, ant-optional, libxerces2-java, libxalan2-java,
libaxis-java, libwsdl4j-java, libgnujaf-java,
libgnumail-java, liblog4j1.2-java, javahelp2,
libcommons-discovery-java, libcommons-logging-java,
- libstevesoft-regex-java, libjmol-java
-Standards-Version: 3.8.0
+ libstevesoft-regex-java, libjmol-java,
+ libcastor-xml-java, libvamsas-client-java,
+ javahelper
+Standards-Version: 3.9.2
Homepage: http://www.jalview.org/
Vcs-Svn: svn://svn.debian.org/svn/pkg-java/trunk/jalview
Vcs-Browser: http://svn.debian.org/viewsvn/pkg-java/trunk/jalview
@@ -17,10 +19,7 @@
Package: jalview
Architecture: all
Depends: ${misc:Depends}, openjdk-6-jre | cacao-oj6-jre | java6-runtime,
- java-wrappers (>= 0.1.11), libxerces2-java, libxalan2-java,
- libaxis-java, libwsdl4j-java, libgnujaf-java, libgnumail-java,
- liblog4j1.2-java, javahelp2, libcommons-discovery-java,
- libcommons-logging-java, libstevesoft-regex-java, libjmol-java
+ java-wrappers (>= 0.1.22), ${java:Depends}
Suggests: kalign, t-coffee, clustalw
Description: multiple alignment editor
JalView is a Java alignement editor that can work with sequence
Added: trunk/jalview/debian/javabuild
===================================================================
--- trunk/jalview/debian/javabuild (rev 0)
+++ trunk/jalview/debian/javabuild 2011-04-14 22:29:53 UTC (rev 13532)
@@ -0,0 +1 @@
+jalview.jar src
Modified: trunk/jalview/debian/new-upstream
===================================================================
--- trunk/jalview/debian/new-upstream 2011-04-14 21:37:44 UTC (rev 13531)
+++ trunk/jalview/debian/new-upstream 2011-04-14 22:29:53 UTC (rev 13532)
@@ -21,23 +21,18 @@
# We repackage the upstream source zip file:
tar xvz -C $dir -f "$filename"
-origname=jalview_$version.dfsg.orig.tar.gz
+origname=jalview_$version.dfsg.orig.tar.bz2
# We repackage excluding the lib/ subdir
cd $dir
# Removing the utils/ directory, not needed for build ?
rm -rf jalview*/utils
-# Remove unneeded jar files.
-for jar in xercesImpl.jar xml-apis.jar saaj.jar axis.jar mail.jar \
- activation.jar wsdl4j.jar jaxrpc.jar log4j-1.2.8.jar jhall.jar \
- commons-discovery.jar commons-logging.jar regex.jar ; do
- rm jalview*/lib/$jar
-done
-echo "Now listing binary jar files still present in the dfsg tarball"
-ls -l jalview*/lib/
+# Removing all binary jars...
+find -name '*.jar' | xargs rm
+
echo "Creating archive"
-tar cvz -f $origname jalview*
+tar cvj -f $origname jalview*
cd -
# We remove any file already existing there: it might be a symlink.
rm -f $orginame
Deleted: trunk/jalview/debian/patches/00list
===================================================================
--- trunk/jalview/debian/patches/00list 2011-04-14 21:37:44 UTC (rev 13531)
+++ trunk/jalview/debian/patches/00list 2011-04-14 22:29:53 UTC (rev 13532)
@@ -1 +0,0 @@
-10-build
\ No newline at end of file
Deleted: trunk/jalview/debian/patches/10-build.dpatch
===================================================================
--- trunk/jalview/debian/patches/10-build.dpatch 2011-04-14 21:37:44 UTC (rev 13531)
+++ trunk/jalview/debian/patches/10-build.dpatch 2011-04-14 22:29:53 UTC (rev 13532)
@@ -1,86 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 10-build.dpatch by <fourmond at debian.org>
-##
-## DP: Mutilate build.xml to disable features that are not necessary
-## DP: for debian package building and that cause FTBS because the
-## DP: files for them are not in the .dfsg tarball.
-
- at DPATCH@
-diff -urNad jalview-2.4.dfsg~/build.xml jalview-2.4.dfsg/build.xml
---- jalview-2.4.dfsg~/build.xml 2008-08-27 14:40:34.000000000 +0200
-+++ jalview-2.4.dfsg/build.xml 2009-01-19 21:14:54.000000000 +0100
-@@ -1,14 +1,14 @@
- <?xml version="1.0"?>
- <project name="jalviewX" default="usage" basedir=".">
- <!-- we use jalopy to format our sources -->
-- <taskdef name="jalopy"
-- classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
-- <classpath>
-- <fileset dir="utils/jalopy/lib">
-- <include name="*.jar" />
-- </fileset>
-- </classpath>
-- </taskdef>
-+<!-- <taskdef name="jalopy" -->
-+<!-- classname="de.hunsicker.jalopy.plugin.ant.AntPlugin"> -->
-+<!-- <classpath> -->
-+<!-- <fileset dir="utils/jalopy/lib"> -->
-+<!-- <include name="*.jar" /> -->
-+<!-- </fileset> -->
-+<!-- </classpath> -->
-+<!-- </taskdef> -->
-
- <target name="help" depends="usage"/>
- <target name="usage">
-@@ -96,10 +96,10 @@
- <property name="wsdl.ClientNS" value="ext.vamsas" />
- <!-- the class path for building the application -->
- <path id="build.classpath">
-- <fileset dir="utils">
-- <include name="*.jar"/>
-- <include name="**/*.jar"/>
-- </fileset>
-+<!-- <fileset dir="utils"> -->
-+<!-- <include name="*.jar"/> -->
-+<!-- <include name="**/*.jar"/> -->
-+<!-- </fileset> -->
- <fileset dir="${libDir}">
- <include name="*.jar"/>
- <include name="**/*.jar"/>
-@@ -123,18 +123,15 @@
- </target>
-
-
-- <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
-- <target name="buildPropertiesFile" depends="init">
-- <tstamp prefix="build">
-- <format property="date" pattern="dd MMMM yyyy"/>
-- </tstamp>
-- <properties file="${outputDir}/.build_properties">
-- <header>
-- ---Jalview Build Details---
-- </header>
-- <property name="VERSION" value="${JALVIEW_VERSION}"/>
-- <property name="BUILD_DATE" value="${build.date}"/>
-- </properties>
-+ <!-- Manual replacement of the property ant task -->
-+ <target name="buildPropertiesFile" depends="init, build">
-+ <tstamp prefix="build">
-+ <format property="date" pattern="dd MMMM yyyy"/>
-+ </tstamp>
-+ <propertyfile file="${outputDir}/.build_properties">
-+ <entry key="VERSION" value="${JALVIEW_VERSION}"/>
-+ <entry key="BUILD_DATE" value="${build.date}"/>
-+ </propertyfile>
- </target>
-
-
-@@ -190,7 +187,7 @@
- unless="help.uptodate">
- <java
- classname="com.sun.java.help.search.Indexer"
-- classpathref="build.classpath"
-+ classpath="/usr/share/java/jhall.jar"
- fork="true"
- dir="${outputDir}/${helpDir}"
- >
Modified: trunk/jalview/debian/rules
===================================================================
--- trunk/jalview/debian/rules 2011-04-14 21:37:44 UTC (rev 13531)
+++ trunk/jalview/debian/rules 2011-04-14 22:29:53 UTC (rev 13532)
@@ -1,67 +1,11 @@
#!/usr/bin/make -f
-# debian/rules for statsvn, based on the one from Batik (uses CDBS)
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+export JAVA_HOME=/usr/lib/jvm/default-java
+export CLASSPATH=/usr/share/java/castor-xml.jar:/usr/share/java/commons-logging.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/castor-core.jar:/usr/share/java/Jmol.jar:/usr/share/java/vamsas-client.jar
-VERSION = $(shell dpkg-parsechangelog | egrep '^Version' | \
- sed -r 's/Version:\s*//' | sed -r 's/^[0-9]+://' | \
- sed -r 's/(\.dfsg)?-[0-9.]+//')
+%:
+ dh $@ --with javahelper
-# export JITC_PROCESSOR_TYPE=6
+override_dh_auto_build:
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/ant.mk
-include /usr/share/cdbs/1/rules/dpatch.mk
-
-JAVA_HOME_DIRS := /usr/lib/jvm/default-java
-ANT_HOME := /usr/share/ant
-DEB_ANT_COMPILER := modern
-DEB_ANT_BUILD_TARGET := build makedist
-DEB_BUILDDIR := .
-DEB_ANT_BUILDFILE := build.xml
-DEB_ANT_CLEAN_TARGET := clean
-
-DEB_JARS := $(ANT_HOME)/lib/ant-nodeps.jar xml-api xercesImpl \
- axis saaj gnumail wsdl4j activation jaxrpc log4j-1.2 \
- jhall Jmol commons-discovery commons-logging regex
-
-
-# Additional arguments for ant, such as properties.
-ANT_ARGS := -DJALVIEW_VERSION=$(VERSION)
-
-# These are jar provided by the source tarball that should be installed
-# along with the program to make it work.
-#
-# AS LONG AS THIS VARIABLE EXISTS, UPLOAD TO MAIN, AND POSSIBLY TO NON-FREE,
-# IS IMPOSSIBLE !
-BINARY_JARS = castor-1.1-cycle-xml.jar \
- vamsas-client.jar
-
-# The source for castor-1.1-cycle-xml.jar can be found at
-# http://dist.codehaus.org/castor/1.1
-#
-# Apparently, jalview works with only the following (newer) files:
-# -> ./castor-1.3.1-xml
-# -> ./castor-1.3.1-core
-#
-# By looking quickly at the src/build.xml file, it sounds as if it is
-# possible to only compile the xml part. Not sure if that makes sense,
-# or even if it would work, though...
-
-print-version:
- echo $(VERSION)
-
-install-binary-jars:
- for jar in $(BINARY_JARS); do \
- install -m 644 lib/$$jar debian/jalview/usr/share/java/jalview-$$jar; \
- done
-
-install/jalview:: install-binary-jars
- install -m 644 dist/jalview.jar debian/jalview/usr/share/java/jalview-$(VERSION).jar
- ln -s jalview-$(VERSION).jar debian/jalview/usr/share/java/jalview.jar
- install -m 755 -t debian/jalview/usr/bin debian/wrappers/jalview
-
-clean::
- rm -rf dist
-
+override_dh_auto_clean:
Added: trunk/jalview/debian/source/format
===================================================================
--- trunk/jalview/debian/source/format (rev 0)
+++ trunk/jalview/debian/source/format 2011-04-14 22:29:53 UTC (rev 13532)
@@ -0,0 +1 @@
+3.0 (quilt)
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