[cdk] 43/62: Prepared 1.2.7-1 release

Emmanuel Bourg ebourg-guest at moszumanska.debian.org
Fri Mar 30 21:56:40 BST 2018


This is an automated email from the git hooks/post-receive script.

ebourg-guest pushed a commit to branch master
in repository cdk.

commit 4cac3e949183aa888d27674ce427d52a17a6e755
Author: Onkar Shinde <onkarshinde at ubuntu.com>
Date:   Sun Apr 17 17:55:48 2011 +0000

    Prepared 1.2.7-1 release
---
 debian/README.source                       |  35 --
 debian/changelog                           |  29 +
 debian/compile.excludes                    |  14 +
 debian/control                             |   6 +-
 debian/libcdk-java.install                 |   1 -
 debian/patches/10-MakeJavafilesFiles.patch |  11 -
 debian/patches/20-Java5.patch              |  11 -
 debian/patches/21_vecmath_lib_name.patch   | 835 ++++++++++++++++-------------
 debian/patches/22_fix_build.patch          | 521 ++++++++++++++++++
 debian/patches/series                      |   2 +
 debian/rules                               |  44 +-
 debian/source/format                       |   1 +
 debian/watch                               |   2 +-
 13 files changed, 1054 insertions(+), 458 deletions(-)

diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 85880c2..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,35 +0,0 @@
-This package uses CDBS (and therefore simple-patchsys.mk) in order to 
-apply patches to the upstream source. Patches are stored in 
-debian/patches and their filenames usually end in .patch or .diff .
-For further details, see the man page for cdbs-edit-patch.
-
-All commands described below should be run from the top directory of the 
-package source tree, unless otherwise stated.
-
- * To generate the fully patched source, in a form ready for
-   editing, that would be built to create Debian packages, run: 
-
-     make -f debian/rules apply-patches
-
-   Note: It has been proposed that, in future, this should happen 
-   automatically when you run dpkg-source -x on a CDBS 
-   simple-patchsys.mk source package.  However, this proposal has 
-   apparently not yet been implemented, so for now you have to do 
-   it yourself like this.
-
- * To modify the source and save those modifications so that
-   they will be applied when building the package, pick a
-   suitably informative patch file name, for example
-   01_add_README.source_file.patch, and then run:
-
-     cdbs-edit-patch 01_add_README.source_file.patch
-
-   This will place you in a new shell in a temporary copy of the 
-   source tree.  Make your desired modifications to it, and then 
-   exit the shell to create the patch file containing them (this 
-   file will appear in debian/patches).
-
- * To remove source modifications that are currently being
-   applied when building the package, run:
-
-     make -f debian/rules reverse-patches
diff --git a/debian/changelog b/debian/changelog
index 89b1e5c..209cdb6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,32 @@
+cdk (1:1.2.7-1) unstable; urgency=low
+
+  * New upstream release. (Closes: #519969)
+  * debian/control
+    - Add build dependency ant-controb, libxpp3-java, r-cran-java.
+    - Update runtime dependency to java5-runtime-headless.
+    - Standards version 3.9.1. No change needed.
+  * debian/patches
+    - series - Use quilt for patches.
+    - 10-MakeJavafilesFiles.patch, 20-Java5.patch - Delete. Not needed anymore.
+    - 21_vecmath_lib_name.patch - Update against current source.
+    - 22_fix_build.patch - New patch to fix build.
+  * debian/compile.excludes
+    - File name patterns to exclude from compilation process. This file is used
+      by 22_fix_build.patch.
+  * debian/rules
+    - Additional 'COMPONENTS' as per current source.
+    - Drop simple-patchsys.mk as we are using source format 3.0.
+  * debian/libcdk-java.install
+    - Remove. Not needed as the install logic is in rules file.
+  * debian/source/format
+    - Switch to source format 3.0.
+  * debian/README.source
+    - Remove. Not needed with source format 3.0.
+  * debian/watch
+    - Keep track of stable versions only.
+
+ -- Onkar Shinde <onkarshinde at ubuntu.com>  Sat, 26 Mar 2011 21:22:40 +0530
+
 cdk (1:1.0.2-5) unstable; urgency=low
 
   * Team upload.
diff --git a/debian/compile.excludes b/debian/compile.excludes
new file mode 100644
index 0000000..dd4c210
--- /dev/null
+++ b/debian/compile.excludes
@@ -0,0 +1,14 @@
+**/InChIGeneratorFactory.java
+**/InChIGenerator.java
+**/InChIToStructure.java
+**/Convertor.java
+**/CMLWriter.java
+**/RssWriter.java
+**/PDBAtomCustomizer.java
+**/MDMoleculeCustomizer.java
+**/R/RModel.java
+**/CNNClassificationModel.java
+**/R/CNNRegressionModel.java
+**/R/LinearRegressionModel.java
+**/PLSRegressionModel.java
+**/QSARCustomizer.java
diff --git a/debian/control b/debian/control
index 18b63a9..8fcd2eb 100644
--- a/debian/control
+++ b/debian/control
@@ -4,15 +4,15 @@ Priority: optional
 Maintainer: Debian Java Maintainers <pkg-java-maintainers at lists.alioth.debian.org>
 Uploaders: Daniel Leidert (dale) <daniel.leidert at wgdd.de>, Michael Koch <konqueror at gmx.de>, Onkar Shinde <onkarshinde at ubuntu.com>
 Build-Depends: cdbs, debhelper (>= 7), default-jdk, ant-optional
-Build-Depends-Indep: antlr, docbook-xsl (>= 1.66.1), javacc, libcommons-cli-java, libcrimson-java, liblog4j1.2-java, libmysql-java, libpgjava, libxerces2-java, xsltproc, libjgrapht0.6-java-link, libvecmath-java, libxom-java, libjama-java
-Standards-Version: 3.8.3
+Build-Depends-Indep: ant-contrib, antlr, docbook-xsl (>= 1.66.1), javacc, libcommons-cli-java, libcrimson-java, liblog4j1.2-java, libmysql-java, libpgjava, libxerces2-java, xsltproc, libjgrapht0.6-java-link, libvecmath-java, libxom-java, libjama-java, libxpp3-java, r-cran-rjava
+Standards-Version: 3.9.1
 Vcs-Svn: svn://svn.debian.org/svn/pkg-java/trunk/cdk
 Vcs-Browser: http://svn.debian.org/wsvn/pkg-java/trunk/cdk
 Homepage: http://cdk.sourceforge.net/
 
 Package: libcdk-java
 Architecture: all
-Depends: default-jre-headless | java2-runtime, ${misc:Depends}
+Depends: default-jre-headless | java5-runtime-headless, ${misc:Depends}
 Suggests: jchempaint, jmol
 Description: Chemistry Development Kit (CDK) Java libraries
  The CDK is a library of Java classes used in computational and
diff --git a/debian/libcdk-java.install b/debian/libcdk-java.install
deleted file mode 100644
index 55a4ee6..0000000
--- a/debian/libcdk-java.install
+++ /dev/null
@@ -1 +0,0 @@
-dist/jar/cdk*.jar usr/share/java
diff --git a/debian/patches/10-MakeJavafilesFiles.patch b/debian/patches/10-MakeJavafilesFiles.patch
deleted file mode 100644
index 62fa05e..0000000
--- a/debian/patches/10-MakeJavafilesFiles.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- cdk-1.0.2.orig/src/net/sf/cdk/tools/MakeJavafilesFiles.java
-+++ cdk-1.0.2/src/net/sf/cdk/tools/MakeJavafilesFiles.java
-@@ -140,7 +140,7 @@
- 				int index = line.indexOf("/**");
- 				if (index != -1) {
- 					inComment = true;
--					if (line.substring(index).indexOf("**/") != -1) inComment = false;
-+					if (line.substring(index).indexOf("*/") != -1) inComment = false;
- 				} else {
- 					if (line.indexOf("*/") != -1) inComment = false;
- 				}
diff --git a/debian/patches/20-Java5.patch b/debian/patches/20-Java5.patch
deleted file mode 100644
index 2bdccc4..0000000
--- a/debian/patches/20-Java5.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- cdk-1.0.2.orig/build.xml
-+++ cdk-1.0.2/build.xml
-@@ -349,7 +349,7 @@
-             <!-- ok, now that we have a copy, compile this copy -->
-             <javac srcdir="${build.src}" destdir="${build}" optimize="${optimization}"
-                     nowarn="${nowarn}"
--                    debug="${debug}" deprecation="${deprecation}" target="1.3" source="1.3">
-+                    debug="${debug}" deprecation="${deprecation}" target="1.5" source="1.5">
-                 <classpath>
-                     <fileset dir="${lib}" >
-                         <exclude name="**/*" unless="module.libdepends.present" />
diff --git a/debian/patches/21_vecmath_lib_name.patch b/debian/patches/21_vecmath_lib_name.patch
index 1a8e83b..cf610ca 100644
--- a/debian/patches/21_vecmath_lib_name.patch
+++ b/debian/patches/21_vecmath_lib_name.patch
@@ -1,459 +1,522 @@
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/build.xml cdk-1.0.2.new/build.xml
---- cdk-1.0.2/build.xml	2009-09-25 17:15:47.000000000 +0530
-+++ cdk-1.0.2.new/build.xml	2009-09-25 17:16:16.000000000 +0530
-@@ -122,7 +122,7 @@
-             <!-- Checks which parts of CDK can be build. -->
+Description: Change vecmath1.2.jar references to vecmath.jar fix the build.
+Forwarded: not-needed
+Author: Onkar Shinde <onshinde at ubuntu.com>
+--- a/build.xml	2011-03-27 14:22:10.000000000 +0530
++++ b/build.xml	2011-03-27 14:23:58.000000000 +0530
+@@ -131,7 +131,7 @@
  
              <!-- test for optional jars -->
--            <available property="vecmath.present" file="${lib}/vecmath1.2-1.14.jar"/>
-+            <available property="vecmath.present" file="${lib}/vecmath.jar"/>
-             <available property="log4j.present" file="${lib}/${log4j.jar}"/>
-             <available property="jgrapht.present" file="${lib}/jgrapht.jar"/>
-             <available property="cmllibs.present" file="${lib}/jumbo52.jar"/>
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/cdk-apps.manifest cdk-1.0.2.new/src/cdk-apps.manifest
---- cdk-1.0.2/src/cdk-apps.manifest	2009-09-25 16:18:38.000000000 +0530
-+++ cdk-1.0.2.new/src/cdk-apps.manifest	2009-09-25 17:35:05.000000000 +0530
-@@ -1,2 +1,2 @@
- Main-Class: org.openscience.cdk.applications.Viewer
--Class-Path: cdk-core.jar cdk-extra.jar cdk-libio.jar gnujaxp.jar batik-awt-util.jar batik-dom.jar batik-util.jar baysmith-io.jar dadml.jar log4j-core.jar log4j.jar mysql-2.0.4.jar postgresql7.0-1.2.jar printf.jar vecmath1.2-1.14.jar xerces-1.3.0.jar jmol.jar joelib.jar
-+Class-Path: cdk-core.jar cdk-extra.jar cdk-libio.jar gnujaxp.jar batik-awt-util.jar batik-dom.jar batik-util.jar baysmith-io.jar dadml.jar log4j-core.jar log4j.jar mysql-2.0.4.jar postgresql7.0-1.2.jar printf.jar vecmath-1.14.jar xerces-1.3.0.jar jmol.jar joelib.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/applications.libdepends cdk-1.0.2.new/src/META-INF/applications.libdepends
---- cdk-1.0.2/src/META-INF/applications.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/applications.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,6 +1,6 @@
- commons-cli.jar
- jfontchooser.jar
- printf.jar
--vecmath1.2.jar
-+vecmath.jar
- xom.jar
- jumbo52.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/builder3d.libdepends cdk-1.0.2.new/src/META-INF/builder3d.libdepends
---- cdk-1.0.2/src/META-INF/builder3d.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/builder3d.libdepends	2009-09-25 17:35:05.000000000 +0530
+             <available property="vecmath.present"
+-                       file="${lib}/vecmath1.2-1.14.jar"/>
++                       file="${lib}/vecmath.jar"/>
+             <available property="log4j.present"
+                        file="${lib}/log4j.jar"/>
+             <available property="jgrapht.present"
+@@ -1158,7 +1158,7 @@
+ 	<classpath>
+ 	  <pathelement location="jar/jgrapht-0.6.0.jar"/>
+           <pathelement location="jar/xercesImpl-2.9.0.jar"/>
+-          <pathelement location="jar/vecmath1.2-1.14.jar"/>
++          <pathelement location="jar/vecmath.jar"/>
+           <pathelement path="${dist}/jar/cdk-builder3dtools.jar" />
+           <pathelement path="${dist}/jar/cdk-interfaces.jar" />
+           <pathelement path="${dist}/jar/cdk-nonotify.jar" />
+--- a/src/META-INF/builder3d.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/builder3d.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,3 +1,3 @@
- jama.jar
--vecmath1.2.jar
+ jama-1.0.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/builder3dtools.libdepends cdk-1.0.2.new/src/META-INF/builder3dtools.libdepends
---- cdk-1.0.2/src/META-INF/builder3dtools.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/builder3dtools.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/builder3dtools.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/builder3dtools.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,2 +1,2 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/charges.libdepends cdk-1.0.2.new/src/META-INF/charges.libdepends
---- cdk-1.0.2/src/META-INF/charges.libdepends	2009-09-25 16:18:38.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/charges.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,2 +1,2 @@
--vecmath1.2.jar
+--- a/src/META-INF/charges.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/charges.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+-vecmath1.2-1.14.jar
 +vecmath.jar
+ jgrapht-0.6.0.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/control.libdepends cdk-1.0.2.new/src/META-INF/control.libdepends
---- cdk-1.0.2/src/META-INF/control.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/control.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/control.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/control.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,2 +1,2 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/datadebug.libdepends cdk-1.0.2.new/src/META-INF/datadebug.libdepends
---- cdk-1.0.2/src/META-INF/datadebug.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/datadebug.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/datadebug.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/datadebug.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1 +1 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/data.libdepends cdk-1.0.2.new/src/META-INF/data.libdepends
---- cdk-1.0.2/src/META-INF/data.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/data.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/data.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/data.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1 +1 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/experimental.libdepends cdk-1.0.2.new/src/META-INF/experimental.libdepends
---- cdk-1.0.2/src/META-INF/experimental.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/experimental.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,2 +1,2 @@
--vecmath1.2.jar
+--- a/src/META-INF/extra.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/extra.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+ jama-1.0.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
- 
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/extra.libdepends cdk-1.0.2.new/src/META-INF/extra.libdepends
---- cdk-1.0.2/src/META-INF/extra.libdepends	2009-09-25 16:18:38.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/extra.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,6 +1,6 @@
- dadml.jar
- jama.jar
--vecmath1.2.jar
-+vecmath.jar
- xindice.jar
- xmldb.jar
- xom.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/forcefield.libdepends cdk-1.0.2.new/src/META-INF/forcefield.libdepends
---- cdk-1.0.2/src/META-INF/forcefield.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/forcefield.libdepends	2009-09-25 17:35:05.000000000 +0530
+ xom-1.1.jar
+--- a/src/META-INF/forcefield.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/forcefield.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,3 +1,3 @@
- jama.jar
--vecmath1.2.jar
+ jama-1.0.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/inchi.libdepends cdk-1.0.2.new/src/META-INF/inchi.libdepends
---- cdk-1.0.2/src/META-INF/inchi.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/inchi.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/inchi.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/inchi.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,4 +1,4 @@
--vecmath1.2.jar
-+vecmath.jar
- xom.jar
- jniinchi-0.4.jar
- jumbo52.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/interfaces.libdepends cdk-1.0.2.new/src/META-INF/interfaces.libdepends
---- cdk-1.0.2/src/META-INF/interfaces.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/interfaces.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1 +1 @@
--vecmath1.2.jar
-+vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/io-jmol.libdepends cdk-1.0.2.new/src/META-INF/io-jmol.libdepends
---- cdk-1.0.2/src/META-INF/io-jmol.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/io-jmol.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,4 +1,4 @@
- jmolApis.jar
- jmolIO.jar
- 
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/io.libdepends cdk-1.0.2.new/src/META-INF/io.libdepends
---- cdk-1.0.2/src/META-INF/io.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/io.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,3 +1,3 @@
--vecmath1.2.jar
+ xom-1.1.jar
+ jniinchi-0.5.jar
+ cmlxom-2.5-b1.jar
+--- a/src/META-INF/interfaces.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/interfaces.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1 +1 @@
+-vecmath1.2-1.14.jar
 +vecmath.jar
- printf.jar
- 
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/jchempaint.applet.libdepends cdk-1.0.2.new/src/META-INF/jchempaint.applet.libdepends
---- cdk-1.0.2/src/META-INF/jchempaint.applet.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/jchempaint.applet.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,5 +1,5 @@
- commons-cli.jar
--vecmath1.2.jar
-+vecmath.jar
- jai_core.jar
- jai_codec.jar
- plugin.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/jchempaint.application.libdepends cdk-1.0.2.new/src/META-INF/jchempaint.application.libdepends
---- cdk-1.0.2/src/META-INF/jchempaint.application.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/jchempaint.application.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,4 +1,4 @@
- commons-cli.jar
--vecmath1.2.jar
-+vecmath.jar
- jai_core.jar
- jai_codec.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/jchempaint.libdepends cdk-1.0.2.new/src/META-INF/jchempaint.libdepends
---- cdk-1.0.2/src/META-INF/jchempaint.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/jchempaint.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,5 +1,5 @@
- commons-cli.jar
--vecmath1.2.jar
-+vecmath.jar
- jai_core.jar
- jai_codec.jar
- jh.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/libio-cml.libdepends cdk-1.0.2.new/src/META-INF/libio-cml.libdepends
---- cdk-1.0.2/src/META-INF/libio-cml.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/libio-cml.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,4 +1,4 @@
--vecmath1.2.jar
+--- a/src/META-INF/io.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/io.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,2 +1,2 @@
+-vecmath1.2-1.14.jar
 +vecmath.jar
- xom.jar
- jumbo52.jar
- 
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/nonotify.libdepends cdk-1.0.2.new/src/META-INF/nonotify.libdepends
---- cdk-1.0.2/src/META-INF/nonotify.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/nonotify.libdepends	2009-09-25 17:35:05.000000000 +0530
+ xpp3-1.1.4c.jar
+--- a/src/META-INF/nonotify.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/nonotify.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1 +1 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/pdb.libdepends cdk-1.0.2.new/src/META-INF/pdb.libdepends
---- cdk-1.0.2/src/META-INF/pdb.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/pdb.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/pdb.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/pdb.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,2 +1,2 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/qsar.libdepends cdk-1.0.2.new/src/META-INF/qsar.libdepends
---- cdk-1.0.2/src/META-INF/qsar.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/qsar.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/qsar.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/qsar.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -2,5 +2,5 @@
  JRI.jar
- jgrapht.jar
- sjava-0.68.jar
--vecmath1.2.jar
-+vecmath.jar
- xom.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/qsar-pdb.libdepends cdk-1.0.2.new/src/META-INF/qsar-pdb.libdepends
---- cdk-1.0.2/src/META-INF/qsar-pdb.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/qsar-pdb.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,5 +1,5 @@
- jama.jar
- jgrapht.jar
+ jgrapht-0.6.0.jar
  sjava-0.68.jar
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
- xom.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/reaction.libdepends cdk-1.0.2.new/src/META-INF/reaction.libdepends
---- cdk-1.0.2/src/META-INF/reaction.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/reaction.libdepends	2009-09-25 17:35:05.000000000 +0530
+ xom-1.1.jar
+--- a/src/META-INF/reaction.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/reaction.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,5 +1,5 @@
- log4j-1.2.jar
- jgrapht.jar
--vecmath1.2.jar
+ log4j.jar
+ jgrapht-0.6.0.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
- xom.jar
+ xom-1.1.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/render.libdepends cdk-1.0.2.new/src/META-INF/render.libdepends
---- cdk-1.0.2/src/META-INF/render.libdepends	2009-09-25 16:18:38.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/render.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/render.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/render.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,2 +1,2 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/sdg.libdepends cdk-1.0.2.new/src/META-INF/sdg.libdepends
---- cdk-1.0.2/src/META-INF/sdg.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/sdg.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/sdg.libdepends	2011-03-27 14:22:02.000000000 +0530
++++ b/src/META-INF/sdg.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,2 +1,2 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
  
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/smiles.libdepends cdk-1.0.2.new/src/META-INF/smiles.libdepends
---- cdk-1.0.2/src/META-INF/smiles.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/smiles.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/smiles.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/smiles.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1 +1 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/standard.libdepends cdk-1.0.2.new/src/META-INF/standard.libdepends
---- cdk-1.0.2/src/META-INF/standard.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/standard.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/standard.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/standard.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,3 +1,3 @@
--vecmath1.2.jar
-+vecmath.jar
- log4j-1.2.jar
- jgrapht.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/structgen.libdepends cdk-1.0.2.new/src/META-INF/structgen.libdepends
---- cdk-1.0.2/src/META-INF/structgen.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/structgen.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1 +1 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-builder3d.libdepends cdk-1.0.2.new/src/META-INF/test-builder3d.libdepends
---- cdk-1.0.2/src/META-INF/test-builder3d.libdepends	2009-09-25 16:18:38.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-builder3d.libdepends	2009-09-25 17:35:05.000000000 +0530
+ log4j.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-builder3d.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/test-builder3d.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,4 +1,4 @@
- jama.jar
--vecmath1.2.jar
-+vecmath.jar
- log4j-1.2.jar
- jgrapht.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-core.libdepends cdk-1.0.2.new/src/META-INF/test-core.libdepends
---- cdk-1.0.2/src/META-INF/test-core.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-core.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,2 +1,2 @@
- log4j-1.2.jar
--vecmath1.2.jar
+ jama-1.0.2.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-core.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/test-core.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+ log4j.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-datadebug.libdepends cdk-1.0.2.new/src/META-INF/test-datadebug.libdepends
---- cdk-1.0.2/src/META-INF/test-datadebug.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-datadebug.libdepends	2009-09-25 17:35:05.000000000 +0530
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-datadebug.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test-datadebug.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,2 +1,2 @@
- log4j-1.2.jar
--vecmath1.2.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-data.libdepends cdk-1.0.2.new/src/META-INF/test-data.libdepends
---- cdk-1.0.2/src/META-INF/test-data.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-data.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/test-data.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test-data.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,2 +1,2 @@
- log4j-1.2.jar
--vecmath1.2.jar
-+vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-experimental.libdepends cdk-1.0.2.new/src/META-INF/test-experimental.libdepends
---- cdk-1.0.2/src/META-INF/test-experimental.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-experimental.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -6,7 +6,7 @@
- log4j-1.2.jar
- printf.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/test-extra.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/test-extra.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -3,5 +3,5 @@
+ cmlxom-2.5-b1.jar
+ log4j.jar
  sjava-0.68.jar
--vecmath1.2.jar
-+vecmath.jar
- xindice.jar
- xmldb.jar
- xom.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-extra.libdepends cdk-1.0.2.new/src/META-INF/test-extra.libdepends
---- cdk-1.0.2/src/META-INF/test-extra.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-extra.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -6,7 +6,7 @@
- log4j-1.2.jar
- printf.jar
- sjava-0.68.jar
--vecmath1.2.jar
-+vecmath.jar
- xindice.jar
- xmldb.jar
- xom.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-forcefield.libdepends cdk-1.0.2.new/src/META-INF/test-forcefield.libdepends
---- cdk-1.0.2/src/META-INF/test-forcefield.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-forcefield.libdepends	2009-09-25 17:35:05.000000000 +0530
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/test-forcefield.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/test-forcefield.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,4 +1,4 @@
- jama.jar
- jgrapht.jar
- log4j-1.2.jar
--vecmath1.2.jar
-+vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-inchi.libdepends cdk-1.0.2.new/src/META-INF/test-inchi.libdepends
---- cdk-1.0.2/src/META-INF/test-inchi.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-inchi.libdepends	2009-09-25 17:35:05.000000000 +0530
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/test-inchi.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test-inchi.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,4 +1,4 @@
--vecmath1.2.jar
-+vecmath.jar
- xom.jar
- jniinchi-0.4.jar
- jumbo52.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-io.libdepends cdk-1.0.2.new/src/META-INF/test-io.libdepends
---- cdk-1.0.2/src/META-INF/test-io.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-io.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -3,7 +3,7 @@
- jumbo52.jar
- log4j-1.2.jar
- printf.jar
--vecmath1.2.jar
-+vecmath.jar
- xindice.jar
- xmldb.jar
- xom.jar
-\ No newline at end of file
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test.libdepends cdk-1.0.2.new/src/META-INF/test.libdepends
---- cdk-1.0.2/src/META-INF/test.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1 +1 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+ jniinchi-0.5.jar
+ cmlxom-2.5-b1.jar
+--- a/src/META-INF/test-io.libdepends	2011-03-27 14:22:02.000000000 +0530
++++ b/src/META-INF/test-io.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,6 +1,6 @@
+ jgrapht-0.6.0.jar
+ cmlxom-2.5-b1.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+ xpp3-1.1.4c.jar
+--- a/src/META-INF/test.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,2 +1,2 @@
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-libiomd.libdepends cdk-1.0.2.new/src/META-INF/test-libiomd.libdepends
---- cdk-1.0.2/src/META-INF/test-libiomd.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-libiomd.libdepends	2009-09-25 17:35:05.000000000 +0530
+ log4j.jar
+--- a/src/META-INF/test-libiomd.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/test-libiomd.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,4 +1,4 @@
--vecmath1.2.jar
-+vecmath.jar
- log4j-1.2.jar
- jumbo52.jar
- xom.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-nonotify.libdepends cdk-1.0.2.new/src/META-INF/test-nonotify.libdepends
---- cdk-1.0.2/src/META-INF/test-nonotify.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-nonotify.libdepends	2009-09-25 17:35:05.000000000 +0530
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ cmlxom-2.5-b1.jar
+ xom-1.1.jar
+--- a/src/META-INF/test-nonotify.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/test-nonotify.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,2 +1,2 @@
- log4j-1.2.jar
--vecmath1.2.jar
-+vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-osjvmts.libdepends cdk-1.0.2.new/src/META-INF/test-osjvmts.libdepends
---- cdk-1.0.2/src/META-INF/test-osjvmts.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-osjvmts.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -6,7 +6,7 @@
- log4j-1.2.jar
- printf.jar
- sjava-0.68.jar
--vecmath1.2.jar
-+vecmath.jar
- xindice.jar
- xmldb.jar
- xom.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-pdb.libdepends cdk-1.0.2.new/src/META-INF/test-pdb.libdepends
---- cdk-1.0.2/src/META-INF/test-pdb.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-pdb.libdepends	2009-09-25 17:35:05.000000000 +0530
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/test-pdb.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/test-pdb.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,4 +1,4 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
  
- log4j-1.2.jar
--vecmath1.2.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-qsarAtomic.libdepends cdk-1.0.2.new/src/META-INF/test-qsarAtomic.libdepends
---- cdk-1.0.2/src/META-INF/test-qsarAtomic.libdepends	2009-09-25 16:18:38.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-qsarAtomic.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,4 +1,4 @@
--vecmath1.2.jar
-+vecmath.jar
- log4j-1.2.jar
- jama.jar
- jgrapht.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-qsarBond.libdepends cdk-1.0.2.new/src/META-INF/test-qsarBond.libdepends
---- cdk-1.0.2/src/META-INF/test-qsarBond.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-qsarBond.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/test-qsar.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/test-qsar.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,4 +1,4 @@
--vecmath1.2.jar
-+vecmath.jar
- log4j-1.2.jar
- jama.jar
- jgrapht.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-qsar.libdepends cdk-1.0.2.new/src/META-INF/test-qsar.libdepends
---- cdk-1.0.2/src/META-INF/test-qsar.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-qsar.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,4 +1,4 @@
--vecmath1.2.jar
-+vecmath.jar
- log4j-1.2.jar
- jama.jar
- jgrapht.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-qsarMolecular.libdepends cdk-1.0.2.new/src/META-INF/test-qsarMolecular.libdepends
---- cdk-1.0.2/src/META-INF/test-qsarMolecular.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-qsarMolecular.libdepends	2009-09-25 17:35:05.000000000 +0530
-@@ -1,4 +1,4 @@
--vecmath1.2.jar
-+vecmath.jar
- log4j-1.2.jar
- jama.jar
- jgrapht.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-reaction.libdepends cdk-1.0.2.new/src/META-INF/test-reaction.libdepends
---- cdk-1.0.2/src/META-INF/test-reaction.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-reaction.libdepends	2009-09-25 17:35:05.000000000 +0530
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-reaction.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/test-reaction.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,5 +1,5 @@
- jama.jar
- jgrapht.jar
- log4j-1.2.jar
--vecmath1.2.jar
-+vecmath.jar
- xom.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-smiles.libdepends cdk-1.0.2.new/src/META-INF/test-smiles.libdepends
---- cdk-1.0.2/src/META-INF/test-smiles.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-smiles.libdepends	2009-09-25 17:35:05.000000000 +0530
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/test-smiles.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/test-smiles.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,5 +1,5 @@
- jgrapht.jar
- log4j-1.2.jar
--vecmath1.2.jar
-+vecmath.jar
- xom.jar
- jumbo52.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-standard.libdepends cdk-1.0.2.new/src/META-INF/test-standard.libdepends
---- cdk-1.0.2/src/META-INF/test-standard.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-standard.libdepends	2009-09-25 17:35:05.000000000 +0530
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+ cmlxom-2.5-b1.jar
+--- a/src/META-INF/test-standard.libdepends	2011-03-27 14:22:02.000000000 +0530
++++ b/src/META-INF/test-standard.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,5 +1,5 @@
+ log4j.jar
+ jgrapht-0.6.0.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ cmlxom-2.5-b1.jar
+ xom-1.1.jar
+--- a/src/META-INF/test-structgen.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test-structgen.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,3 +1,3 @@
- log4j-1.2.jar
- jgrapht.jar
--vecmath1.2.jar
+ log4j.jar
+ jgrapht-0.6.0.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-structgen.libdepends cdk-1.0.2.new/src/META-INF/test-structgen.libdepends
---- cdk-1.0.2/src/META-INF/test-structgen.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-structgen.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/test-valencycheck.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test-valencycheck.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,3 +1,3 @@
- log4j-1.2.jar
- jgrapht.jar
--vecmath1.2.jar
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/valencycheck.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/valencycheck.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1 +1 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/diff.libdepends	2011-03-27 14:22:02.000000000 +0530
++++ b/src/META-INF/diff.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1 +1 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/fingerprint.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/fingerprint.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1 +1 @@
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/test-valencycheck.libdepends cdk-1.0.2.new/src/META-INF/test-valencycheck.libdepends
---- cdk-1.0.2/src/META-INF/test-valencycheck.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/test-valencycheck.libdepends	2009-09-25 17:35:05.000000000 +0530
+--- a/src/META-INF/formula.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/formula.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,2 +1,2 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ 
+--- a/src/META-INF/isomorphism.libdepends	2011-03-27 14:22:02.000000000 +0530
++++ b/src/META-INF/isomorphism.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1,3 +1,3 @@
- jgrapht.jar
- log4j-1.2.jar
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
-diff -Nur -x '*.orig' -x '*~' cdk-1.0.2/src/META-INF/valencycheck.libdepends cdk-1.0.2.new/src/META-INF/valencycheck.libdepends
---- cdk-1.0.2/src/META-INF/valencycheck.libdepends	2009-09-25 16:18:39.000000000 +0530
-+++ cdk-1.0.2.new/src/META-INF/valencycheck.libdepends	2009-09-25 17:35:05.000000000 +0530
+ log4j.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/libiocml.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/libiocml.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,4 +1,4 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+ cmlxom-2.5-b1.jar
+ 
+--- a/src/META-INF/pcore.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/pcore.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,2 +1,2 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/qm.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/qm.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1 +1 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/qsaratomic.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/qsaratomic.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -2,5 +2,5 @@
+ JRI.jar
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/qsarbond.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/qsarbond.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -2,5 +2,5 @@
+ JRI.jar
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/qsarmolecular.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/qsarmolecular.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -2,5 +2,5 @@
+ JRI.jar
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/qsarprotein.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/qsarprotein.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -2,5 +2,5 @@
+ JRI.jar
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/smarts.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/smarts.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1 +1 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/test-atomtype.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/test-atomtype.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-charges.libdepends	2011-03-27 14:22:02.000000000 +0530
++++ b/src/META-INF/test-charges.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-diff.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/test-diff.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,2 +1,2 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+--- a/src/META-INF/test-fingerprint.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/test-fingerprint.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ jgrapht-0.6.0.jar
+ log4j.jar
+--- a/src/META-INF/test-formula.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test-formula.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,5 +1,5 @@
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/test-interfaces.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/test-interfaces.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,2 +1,2 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+--- a/src/META-INF/test-ioformats.libdepends	2011-03-27 14:22:03.000000000 +0530
++++ b/src/META-INF/test-ioformats.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,6 +1,6 @@
+ jgrapht-0.6.0.jar
+ cmlxom-2.5-b1.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+ xpp3-1.1.4c.jar
+--- a/src/META-INF/test-ionpot.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test-ionpot.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,5 +1,5 @@
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/test-isomorphism.libdepends	2011-03-27 14:21:59.000000000 +0530
++++ b/src/META-INF/test-isomorphism.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-libiocml.libdepends	2011-03-27 14:22:05.000000000 +0530
++++ b/src/META-INF/test-libiocml.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,4 +1,4 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ cmlxom-2.5-b1.jar
+ xom-1.1.jar
+--- a/src/META-INF/test-pcore.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/test-pcore.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,4 +1,4 @@
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ xom-1.1.jar
+--- a/src/META-INF/test-qm.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/test-qm.libdepends	2011-03-27 14:22:23.000000000 +0530
 @@ -1 +1 @@
--vecmath1.2.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/test-qsaratomic.libdepends	2011-03-27 14:22:02.000000000 +0530
++++ b/src/META-INF/test-qsaratomic.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,4 +1,4 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-qsarbond.libdepends	2011-03-27 14:21:58.000000000 +0530
++++ b/src/META-INF/test-qsarbond.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,4 +1,4 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-qsarionpot.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/test-qsarionpot.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,4 +1,4 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-qsarmolecular.libdepends	2011-03-27 14:22:01.000000000 +0530
++++ b/src/META-INF/test-qsarmolecular.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,4 +1,4 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-qsarprotein.libdepends	2011-03-27 14:22:02.000000000 +0530
++++ b/src/META-INF/test-qsarprotein.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,4 +1,4 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ log4j.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-render.libdepends	2011-03-27 14:22:05.000000000 +0530
++++ b/src/META-INF/test-render.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,2 +1,2 @@
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- a/src/META-INF/test-sdg.libdepends	2011-03-27 14:22:04.000000000 +0530
++++ b/src/META-INF/test-sdg.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-smarts.libdepends	2011-03-27 14:22:00.000000000 +0530
++++ b/src/META-INF/test-smarts.libdepends	2011-03-27 14:22:23.000000000 +0530
+@@ -1,3 +1,3 @@
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.jar
 +vecmath.jar
diff --git a/debian/patches/22_fix_build.patch b/debian/patches/22_fix_build.patch
new file mode 100644
index 0000000..a19e2c9
--- /dev/null
+++ b/debian/patches/22_fix_build.patch
@@ -0,0 +1,521 @@
+Description: Disable components which fail to build because of yet unpackaged
+ build dependencies. Also change references to certain build dependencies as
+ per names in system.
+Forwarded: not-needed
+Author: Onkar Shinde <onshinde at ubuntu.com>
+--- a/build.xml	2011-04-17 15:36:32.000000000 +0530
++++ b/build.xml	2011-04-17 15:40:05.000000000 +0530
+@@ -39,7 +39,7 @@
+     <!-- Include the ant-contrib goodies -->
+     <taskdef resource="net/sf/antcontrib/antlib.xml">
+         <classpath>
+-            <pathelement location="${basedir}/develjar/ant-contrib-1.0b3.jar"/>
++            <pathelement location="/usr/share/java/ant-contrib.jar"/>
+         </classpath>
+     </taskdef>
+ 
+@@ -133,7 +133,7 @@
+             <available property="vecmath.present"
+                        file="${lib}/vecmath.jar"/>
+             <available property="log4j.present"
+-                       file="${lib}/log4j.jar"/>
++                       file="${lib}/log4j-1.2.jar"/>
+             <available property="jgrapht.present"
+                        file="${lib}/jgrapht-0.6.0.jar"/>
+ 
+@@ -362,13 +362,17 @@
+             </copy>
+ 
+             <!-- ok, now that we have a copy, compile this copy -->
+-            <javac srcdir="${build.src}/${module}" destdir="${build}/${module}" optimize="${optimization}"
++            <javac sourcepath="" srcdir="${build.src}/${module}" destdir="${build}/${module}" optimize="${optimization}"
+                     debug="${debug}" deprecation="${deprecation}" target="1.5" source="1.5">
+                 <classpath>
+                     <fileset dir="${lib}" >
+                         <exclude name="**/*" unless="module.libdepends.present" />
+                         <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
+                     </fileset>
++                    <fileset dir="/usr/lib/R/site-library/rJava/jri" >
++                        <exclude name="**/*" unless="module.libdepends.present" />
++                        <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
++                    </fileset>
+                     <fileset dir="${devellib}">
+                         <exclude name="**/*" unless="module.devellibdepends.present" />
+                         <includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
+@@ -387,6 +391,7 @@
+ 
+                 <includesfile name="${build}/${module}.javafiles"/>
+                 <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
++                <excludesfile name="debian/compile.excludes"/>
+             </javac>
+ 
+         	<!-- create a autogenerated.classes file, if applicable, so that these files can be included in the jar -->
+@@ -405,7 +410,7 @@
+             <!-- and then jar things up into the module jar -->
+             <jar jarfile="${dist}/jar/cdk-${module}.jar">
+                <fileset dir="${build}/${module}">
+-                    <includesfile name="${build}/${module}.classes" />
++                    <include name="**/*.class" />
+                     <includesfile name="${build}/${module}.autogenerated.classes" if="module.autogenerated.present"/>
+                     <excludesfile name="${build}/java1.4+.classes" if="isJava13"/>
+                     <!-- excludesfile name="${build}/java1.4.classes" unless="isJava14"/ -->
+@@ -468,8 +473,8 @@
+ 	 <!-- OK, we now need to do some replacements such as 
+ 	      adding cdk.module tags and changing access modes
+ 	  -->
+-	 <replace file="${src}/main/org/openscience/cdk/smiles/smarts/parser/JJTSMARTSParserState.java" 
+-	          token="class JJTSMARTSParserState {" value="public class JJTSMARTSParserState {" />
++	 <!--replace file="${src}/main/org/openscience/cdk/smiles/smarts/parser/JJTSMARTSParserState.java"
++	          token="class JJTSMARTSParserState {" value="public class JJTSMARTSParserState {" /-->
+          <replace dir="${src}/main/org/openscience/cdk/smiles/smarts/parser" 
+ 	          excludes="AST*.java,SMARTSParser.jjt,SMARTSParser.jj,*Node.java"
+                   token="package org.openscience.cdk.smiles.smarts.parser;" summary="true" >
+--- a/src/META-INF/atomtype.libdepends	2011-04-17 15:13:30.000000000 +0530
++++ b/src/META-INF/atomtype.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1 +1 @@
+-log4j.jar
++log4j-1.2.jar
+--- a/src/META-INF/core.libdepends	2011-04-17 15:13:27.000000000 +0530
++++ b/src/META-INF/core.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1 +1 @@
+-log4j.jar
++log4j-1.2.jar
+--- a/src/META-INF/isomorphism.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/isomorphism.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/reaction.libdepends	2011-04-17 15:36:32.000000000 +0530
++++ b/src/META-INF/reaction.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,5 +1,5 @@
+-log4j.jar
++log4j-1.2.jar
+ jgrapht-0.6.0.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+ 
+--- a/src/META-INF/standard.libdepends	2011-04-17 15:36:32.000000000 +0530
++++ b/src/META-INF/standard.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-atomtype.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-atomtype.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-builder3d.libdepends	2011-04-17 15:36:32.000000000 +0530
++++ b/src/META-INF/test-builder3d.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,4 +1,4 @@
+ jama-1.0.2.jar
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-charges.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-charges.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-core.libdepends	2011-04-17 15:36:32.000000000 +0530
++++ b/src/META-INF/test-core.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-data.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-data.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+--- a/src/META-INF/test-datadebug.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-datadebug.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+--- a/src/META-INF/test-diff.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-diff.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+--- a/src/META-INF/test-extra.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-extra.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,7 +1,7 @@
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+ cmlxom-2.5-b1.jar
+-log4j.jar
++log4j-1.2.jar
+ sjava-0.68.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/test-fingerprint.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-fingerprint.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+ vecmath.jar
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+--- a/src/META-INF/test-forcefield.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-forcefield.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,4 +1,4 @@
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+--- a/src/META-INF/test-formula.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-formula.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,5 +1,5 @@
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/test-inchi.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-inchi.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,5 +1,5 @@
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+ jniinchi-0.5.jar
+ cmlxom-2.5-b1.jar
+-log4j.jar
++log4j-1.2.jar
+--- a/src/META-INF/test-interfaces.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-interfaces.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+--- a/src/META-INF/test-io.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-io.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,6 +1,6 @@
+ jgrapht-0.6.0.jar
+ cmlxom-2.5-b1.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+ xpp3-1.1.4c.jar
+--- a/src/META-INF/test-ioformats.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-ioformats.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,6 +1,6 @@
+ jgrapht-0.6.0.jar
+ cmlxom-2.5-b1.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+ xpp3-1.1.4c.jar
+--- a/src/META-INF/test-ionpot.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-ionpot.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,5 +1,5 @@
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/test-isomorphism.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-isomorphism.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-libiocml.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-libiocml.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,5 +1,5 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ cmlxom-2.5-b1.jar
+-xom-1.1.jar
++xom.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-libiomd.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-libiomd.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,4 +1,4 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ cmlxom-2.5-b1.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/test-nonotify.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-nonotify.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+--- a/src/META-INF/test-pcore.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-pcore.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,4 +1,4 @@
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/test-pdb.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-pdb.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,4 +1,4 @@
+ vecmath.jar
+ 
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+--- a/src/META-INF/test-qsar.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-qsar.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,7 +1,7 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-xom-1.1.jar
++xom.jar
+ JRI.jar
+ sjava-0.68.jar
+--- a/src/META-INF/test-qsaratomic.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-qsaratomic.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,7 +1,7 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-xom-1.1.jar
++xom.jar
+ JRI.jar
+ sjava-0.68.jar
+--- a/src/META-INF/test-qsarbond.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-qsarbond.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,7 +1,7 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-xom-1.1.jar
++xom.jar
+ JRI.jar
+ sjava-0.68.jar
+--- a/src/META-INF/test-qsarionpot.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-qsarionpot.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,7 +1,7 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-xom-1.1.jar
++xom.jar
+ JRI.jar
+ sjava-0.68.jar
+--- a/src/META-INF/test-qsarmolecular.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-qsarmolecular.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,7 +1,7 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-xom-1.1.jar
++xom.jar
+ JRI.jar
+ sjava-0.68.jar
+--- a/src/META-INF/test-qsarprotein.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-qsarprotein.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,7 +1,7 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-xom-1.1.jar
++xom.jar
+ JRI.jar
+ sjava-0.68.jar
+--- a/src/META-INF/test-reaction.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-reaction.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,5 +1,5 @@
+ jama-1.0.2.jar
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/test-render.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-render.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+--- a/src/META-INF/test-sdg.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-sdg.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+ jgrapht-0.6.0.jar
+--- a/src/META-INF/test-smarts.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-smarts.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+--- a/src/META-INF/test-smiles.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-smiles.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,5 +1,5 @@
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+ cmlxom-2.5-b1.jar
+--- a/src/META-INF/test-standard.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-standard.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,5 +1,5 @@
+-log4j.jar
++log4j-1.2.jar
+ jgrapht-0.6.0.jar
+ vecmath.jar
+ cmlxom-2.5-b1.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/test-structgen.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-structgen.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+-log4j.jar
++log4j-1.2.jar
+ jgrapht-0.6.0.jar
+ vecmath.jar
+--- a/src/META-INF/test-valencycheck.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test-valencycheck.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+ jgrapht-0.6.0.jar
+-log4j.jar
++log4j-1.2.jar
+ vecmath.jar
+--- a/src/META-INF/test.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/test.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+ vecmath.jar
+-log4j.jar
++log4j-1.2.jar
+--- a/src/META-INF/dict.libdepends	2011-04-17 15:13:29.000000000 +0530
++++ b/src/META-INF/dict.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1 +1 @@
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/extra.libdepends	2011-04-17 15:36:32.000000000 +0530
++++ b/src/META-INF/extra.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,3 +1,3 @@
+ jama-1.0.2.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/inchi.libdepends	2011-04-17 15:36:32.000000000 +0530
++++ b/src/META-INF/inchi.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,4 +1,4 @@
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+ jniinchi-0.5.jar
+ cmlxom-2.5-b1.jar
+--- a/src/META-INF/libiocml.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/libiocml.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,4 +1,4 @@
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+ cmlxom-2.5-b1.jar
+ 
+--- a/src/META-INF/libiomd.libdepends	2011-04-17 15:13:27.000000000 +0530
++++ b/src/META-INF/libiomd.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+ cmlxom-2.5-b1.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/pcore.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/pcore.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/pdbcml.libdepends	2011-04-17 15:13:29.000000000 +0530
++++ b/src/META-INF/pdbcml.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+-xom-1.1.jar
++xom.jar
+ cmlxom-2.5-b1.jar
+--- a/src/META-INF/qsar.libdepends	2011-04-17 15:36:32.000000000 +0530
++++ b/src/META-INF/qsar.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -3,4 +3,4 @@
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/qsaratomic.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/qsaratomic.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -3,4 +3,4 @@
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/qsarbond.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/qsarbond.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -3,4 +3,4 @@
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/qsarcml.libdepends	2011-04-17 15:13:30.000000000 +0530
++++ b/src/META-INF/qsarcml.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -1,2 +1,2 @@
+-xom-1.1.jar
++xom.jar
+ cmlxom-2.5-b1.jar
+--- a/src/META-INF/qsarmolecular.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/qsarmolecular.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -3,4 +3,4 @@
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
+--- a/src/META-INF/qsarprotein.libdepends	2011-04-17 15:36:33.000000000 +0530
++++ b/src/META-INF/qsarprotein.libdepends	2011-04-17 15:36:33.000000000 +0530
+@@ -3,4 +3,4 @@
+ jgrapht-0.6.0.jar
+ sjava-0.68.jar
+ vecmath.jar
+-xom-1.1.jar
++xom.jar
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c762564
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+21_vecmath_lib_name.patch
+22_fix_build.patch
diff --git a/debian/rules b/debian/rules
index 93b8dd5..c9d6eec 100644
--- a/debian/rules
+++ b/debian/rules
@@ -2,39 +2,63 @@
 
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/ant.mk
-include /usr/share/cdbs/1/rules/simple-patchsys.mk
 
 JAVA_HOME := /usr/lib/jvm/default-java
 DEB_JARS := \
+	ant-contrib \
 	ant-nodeps \
 	javacc \
 	vecmath \
 	log4j-1.2 \
 	commons-cli
 
+ANT_ARGS := -Dlib=/usr/share/java
+
 DEB_ANT_BUILD_TARGET := info dist-all
 
 COMPONENTS := \
-	applications \
+	annotation \
+	atomtype \
 	builder3d \
+	builder3dtools \
+	charges \
+	control \
 	core \
-	controller \
 	data \
-	experimental \
+	dict \
+	diff \
 	extra \
+	fingerprint \
+	forcefield \
+	formula \
+	inchi \
 	interfaces \
+	ioformats \
 	io \
-	libio-cml \
-	layout \
-	pdb-cml \
+	ionpot \
+	isomorphism \
+	libiocml \
+	libiomd \
+	nonotify \
+	pcore \
+	pdbcml \
 	pdb \
-	qsar-cml \
+	qm \
 	qsar \
-	qsar-pdb \
+	qsaratomic \
+	qsarbond \
+	qsarcml \
+	qsarionpot \
+	qsarmolecular \
+	qsarprotein \
+	reaction \
 	render \
+	sdg \
+	smarts \
+	smiles \
 	standard \
 	structgen \
-	swing 
+	valencycheck
 
 clean::
 	rm -f src/org/openscience/cdk/smiles/smarts/parser/SMARTSParserTokenManager.java
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
index 6239b5f..f882c61 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,2 @@
 version=3
-http://sf.net/cdk/ cdk-(\d+\..+)\.tar\.gz
+http://sf.net/cdk/ cdk-(1\.2[\d\.]+)\.tar\.gz debian uupdate

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-java/cdk.git



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