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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Uploaders: Daniel Leidert (dale) <[email protected]>, Michael Koch <[email protected]>, Onkar Shinde <[email protected]> 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 <[email protected]> +--- 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 <[email protected]> +--- 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 _______________________________________________ pkg-java-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits
