[pkg-java] r13548 - in trunk/cdk/debian: . patches source
Onkar Shinde
onkarshinde-guest at alioth.debian.org
Sun Apr 17 17:55:51 UTC 2011
Author: onkarshinde-guest
Date: 2011-04-17 17:55:48 +0000 (Sun, 17 Apr 2011)
New Revision: 13548
Added:
trunk/cdk/debian/compile.excludes
trunk/cdk/debian/patches/22_fix_build.patch
trunk/cdk/debian/patches/series
trunk/cdk/debian/source/
trunk/cdk/debian/source/format
Removed:
trunk/cdk/debian/README.source
trunk/cdk/debian/libcdk-java.install
trunk/cdk/debian/patches/10-MakeJavafilesFiles.patch
trunk/cdk/debian/patches/20-Java5.patch
Modified:
trunk/cdk/debian/changelog
trunk/cdk/debian/control
trunk/cdk/debian/patches/21_vecmath_lib_name.patch
trunk/cdk/debian/rules
trunk/cdk/debian/watch
Log:
Prepared 1.2.7-1 release
Deleted: trunk/cdk/debian/README.source
===================================================================
--- trunk/cdk/debian/README.source 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/README.source 2011-04-17 17:55:48 UTC (rev 13548)
@@ -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
Modified: trunk/cdk/debian/changelog
===================================================================
--- trunk/cdk/debian/changelog 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/changelog 2011-04-17 17:55:48 UTC (rev 13548)
@@ -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.
Added: trunk/cdk/debian/compile.excludes
===================================================================
--- trunk/cdk/debian/compile.excludes (rev 0)
+++ trunk/cdk/debian/compile.excludes 2011-04-17 17:55:48 UTC (rev 13548)
@@ -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
Modified: trunk/cdk/debian/control
===================================================================
--- trunk/cdk/debian/control 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/control 2011-04-17 17:55:48 UTC (rev 13548)
@@ -4,15 +4,15 @@
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, ${misc:Depends}
Suggests: jchempaint, jmol
Description: Chemistry Development Kit (CDK) Java libraries
The CDK is a library of Java classes used in computational and
Deleted: trunk/cdk/debian/libcdk-java.install
===================================================================
--- trunk/cdk/debian/libcdk-java.install 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/libcdk-java.install 2011-04-17 17:55:48 UTC (rev 13548)
@@ -1 +0,0 @@
-dist/jar/cdk*.jar usr/share/java
Deleted: trunk/cdk/debian/patches/10-MakeJavafilesFiles.patch
===================================================================
--- trunk/cdk/debian/patches/10-MakeJavafilesFiles.patch 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/patches/10-MakeJavafilesFiles.patch 2011-04-17 17:55:48 UTC (rev 13548)
@@ -1,11 +0,0 @@
---- cdk-1.0.2.orig/src/net/sf/cdk/tools/MakeJavafilesFiles.java
-+++ cdk-1.0.2/src/net/sf/cdk/tools/MakeJavafilesFiles.java
-@@ -140,7 +140,7 @@
- int index = line.indexOf("/**");
- if (index != -1) {
- inComment = true;
-- if (line.substring(index).indexOf("**/") != -1) inComment = false;
-+ if (line.substring(index).indexOf("*/") != -1) inComment = false;
- } else {
- if (line.indexOf("*/") != -1) inComment = false;
- }
Deleted: trunk/cdk/debian/patches/20-Java5.patch
===================================================================
--- trunk/cdk/debian/patches/20-Java5.patch 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/patches/20-Java5.patch 2011-04-17 17:55:48 UTC (rev 13548)
@@ -1,11 +0,0 @@
---- cdk-1.0.2.orig/build.xml
-+++ cdk-1.0.2/build.xml
-@@ -349,7 +349,7 @@
- <!-- ok, now that we have a copy, compile this copy -->
- <javac srcdir="${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" />
Modified: trunk/cdk/debian/patches/21_vecmath_lib_name.patch
===================================================================
--- trunk/cdk/debian/patches/21_vecmath_lib_name.patch 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/patches/21_vecmath_lib_name.patch 2011-04-17 17:55:48 UTC (rev 13548)
@@ -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
+-vecmath1.2-1.14.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
+ 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.jar
+-vecmath1.2-1.14.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
+--- 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
-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
-+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
-+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
+ 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/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
+ 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 @@
- jama.jar
- jgrapht.jar
- sjava-0.68.jar
--vecmath1.2.jar
+ log4j.jar
+ jgrapht-0.6.0.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
-@@ -1,5 +1,5 @@
- log4j-1.2.jar
- jgrapht.jar
--vecmath1.2.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
+-vecmath1.2-1.14.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
-+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
+ jama-1.0.2.jar
+-vecmath1.2-1.14.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
+ 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
+ log4j.jar
+-vecmath1.2-1.14.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
+--- 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
+-vecmath1.2-1.14.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
+ 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-1.0.2.jar
+ jgrapht-0.6.0.jar
+ log4j.jar
+-vecmath1.2-1.14.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
+--- 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 @@
- jama.jar
- 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/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
+ 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
+ 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
+-vecmath1.2-1.14.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
+ 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.jar
+-vecmath1.2-1.14.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
+--- 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 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+
+ log4j.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- 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 @@
+-vecmath1.2-1.14.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-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-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.jar
+ jgrapht-0.6.0.jar
+-vecmath1.2-1.14.jar
++vecmath.jar
+--- 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 @@
+ 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.jar
+-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
+--- 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
+--- 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 @@
+-vecmath1.2-1.14.jar
++vecmath.jar
+ 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.jar
+-vecmath1.2-1.14.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
+ 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 @@
- 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/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
+ 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.jar
+-vecmath1.2-1.14.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
+ 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.jar
+-vecmath1.2-1.14.jar
+vecmath.jar
-
- log4j-1.2.jar
--vecmath1.2.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
-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
+ 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 @@
+-vecmath1.2-1.14.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.jar
+-vecmath1.2-1.14.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
+ 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.jar
+-vecmath1.2-1.14.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
+ 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.jar
+-vecmath1.2-1.14.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
+ 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.jar
+-vecmath1.2-1.14.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
-@@ -1,5 +1,5 @@
- jama.jar
- jgrapht.jar
- log4j-1.2.jar
--vecmath1.2.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
- 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
-@@ -1,5 +1,5 @@
- jgrapht.jar
- log4j-1.2.jar
--vecmath1.2.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
- 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
+--- 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-1.2.jar
- jgrapht.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-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
+ 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 @@
- log4j-1.2.jar
- jgrapht.jar
--vecmath1.2.jar
+ jgrapht-0.6.0.jar
+ log4j.jar
+-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
-@@ -1,3 +1,3 @@
- jgrapht.jar
- log4j-1.2.jar
--vecmath1.2.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
-@@ -1 +1 @@
--vecmath1.2.jar
-+vecmath.jar
Added: trunk/cdk/debian/patches/22_fix_build.patch
===================================================================
--- trunk/cdk/debian/patches/22_fix_build.patch (rev 0)
+++ trunk/cdk/debian/patches/22_fix_build.patch 2011-04-17 17:55:48 UTC (rev 13548)
@@ -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
Added: trunk/cdk/debian/patches/series
===================================================================
--- trunk/cdk/debian/patches/series (rev 0)
+++ trunk/cdk/debian/patches/series 2011-04-17 17:55:48 UTC (rev 13548)
@@ -0,0 +1,2 @@
+21_vecmath_lib_name.patch
+22_fix_build.patch
Modified: trunk/cdk/debian/rules
===================================================================
--- trunk/cdk/debian/rules 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/rules 2011-04-17 17:55:48 UTC (rev 13548)
@@ -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
Added: trunk/cdk/debian/source/format
===================================================================
--- trunk/cdk/debian/source/format (rev 0)
+++ trunk/cdk/debian/source/format 2011-04-17 17:55:48 UTC (rev 13548)
@@ -0,0 +1 @@
+3.0 (quilt)
Modified: trunk/cdk/debian/watch
===================================================================
--- trunk/cdk/debian/watch 2011-04-17 17:35:02 UTC (rev 13547)
+++ trunk/cdk/debian/watch 2011-04-17 17:55:48 UTC (rev 13548)
@@ -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
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