From 1ebfca0a01e67fe531c1774aef55c303664eb167 Mon Sep 17 00:00:00 2001
From: Susi Lehtola <jussilehtola@fedoraproject.org>
Date: Aug 10 2013 17:49:02 +0000
Subject: Update to 13.2.3.


---

diff --git a/.gitignore b/.gitignore
index 453304d..5bd67aa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,4 @@ jmol-11.8.26-full.tar.gz
 /Jmol-12.0.41-full.tar.gz
 /Jmol-12.0.48-full.tar.gz
 /Jmol-13.0.15-full.tar.gz
+/Jmol-13.2.3-full.tar.gz
diff --git a/jmol-13.0.12-dontsign.patch b/jmol-13.0.12-dontsign.patch
deleted file mode 100644
index 0917b9c..0000000
--- a/jmol-13.0.12-dontsign.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff -up jmol-13.0.12/build.xml.orig jmol-13.0.12/build.xml
---- jmol-13.0.12/build.xml.orig	2013-03-25 16:33:14.752898377 +0200
-+++ jmol-13.0.12/build.xml	2013-03-25 16:34:52.979914361 +0200
-@@ -430,13 +430,14 @@ all support for previous versions remove
-       <fileset dir="${appjars.dir}" includes="**/*"/>
-       <fileset dir="src/org/jmol/translation/Jmol" includes="Messages*.class"/>
-     </jar>
--    <signjar jar="${jmol.build.dir}/JmolUnsigned.jar"
-+    
-+    <!--<signjar jar="${jmol.build.dir}/JmolUnsigned.jar"
-              signedjar="${jmol.build.dir}/Jmol.jar"
-              keystore="selfSignedCertificate/selfSignedCertificate.store"
--             storepass="selfSignedCertificate" alias="selfSignedCertificate" />
-+             storepass="selfSignedCertificate" alias="selfSignedCertificate" />-->
-     <!-- to verify that a .jar file is signed: jarsigner -verify foo.jar -->
-   	
--    <delete file="${jmol.build.dir}/JmolUnsigned.jar"/>
-+    <!--    <delete file="${jmol.build.dir}/JmolUnsigned.jar"/> -->
-     <jar destfile="${jmol.build.dir}/JmolUnsignedF.jar"
-          manifest="manifest/applicationData.txt">
-       <fileset dir="${classes.dir}" >
-@@ -463,13 +464,13 @@ all support for previous versions remove
-       <fileset dir="${appjars.dir}" includes="**/cli/** **/vecmath/** **/naga/**" />
-       <fileset dir="src/org/jmol/translation/Jmol" includes="Messages*.class"/>
-     </jar>
--    <signjar jar="${jmol.build.dir}/JmolUnsignedF.jar"
-+    <!--<signjar jar="${jmol.build.dir}/JmolUnsignedF.jar"
-              signedjar="${jmol.build.dir}/JmolData.jar"
-              keystore="selfSignedCertificate/selfSignedCertificate.store"
--             storepass="selfSignedCertificate" alias="selfSignedCertificate" />
-+             storepass="selfSignedCertificate" alias="selfSignedCertificate" />-->
-     <!-- to verify that a .jar file is signed: jarsigner -verify foo.jar -->
- 
--  	<delete file="${jmol.build.dir}/JmolUnsignedF.jar"/>
-+    <!--<delete file="${jmol.build.dir}/JmolUnsignedF.jar"/>-->
-     <copy todir="${jmol.build.dir}">
-       <fileset dir=".">
-         <include name="jmol" />
diff --git a/jmol-13.0.12-fedorabuild.patch b/jmol-13.0.12-fedorabuild.patch
deleted file mode 100644
index 3c89f86..0000000
--- a/jmol-13.0.12-fedorabuild.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff -up jmol-13.0.12/build.xml.orig jmol-13.0.12/build.xml
---- jmol-13.0.12/build.xml.orig	2013-01-25 09:03:22.000000000 +0200
-+++ jmol-13.0.12/build.xml	2013-03-25 18:35:58.477352422 +0200
-@@ -40,7 +40,7 @@
-   <property name="jvxl_version" value="0.1" />
- 
-   <property name="tests.source.dir" value="source-tests" />
--  <property name="lib.dir" value="jars" />
-+  <property name="lib.dir" value="/usr/share/java" />
-   <property name="plugin.dir" value="plugin-jars" />
-   <property name="appjars.dir" value="build/appjars" />
-   <property name="classes.dir" value="build/classes" />
-@@ -54,10 +54,10 @@
-   <property name="jmol.build.dir" value="build" />
-   <property name="docbook-xsl" value="docbook-xsl-1.76.1" />
-   <property name="docbook-xml" value="docbook-xml-4.4" />
--  <property name="vecmath.jar" value="vecmath1.2-1.14.jar" />
--  <property name="naga.jar" value="naga-3_0.jar" />
--  <property name="itext.jar" value="itext-1.4.5.jar" />
--  <property name="commons-cli.jar" value="commons-cli-1.0.jar" />
-+  <property name="vecmath.jar" value="vecmath.jar" />
-+  <property name="naga.jar" value="naga.jar" />
-+  <property name="itext.jar" value="itext.jar" />
-+  <property name="commons-cli.jar" value="commons-cli.jar" />
-   <property name="saxon.jar" value="saxon.jar" />
-   <property name="saxon.main" value="com.icl.saxon.StyleSheet" />
- 
-@@ -363,7 +363,7 @@ all support for previous versions remove
-           <!-- srcfiles dir="${lib.dir}" includes="Acme.jar"/ -->
-           <srcfiles dir="${lib.dir}" includes="${itext.jar}"/>
-           <srcfiles dir="${lib.dir}" includes="${commons-cli.jar}"/>
--          <srcfiles dir="${lib.dir}" includes="JSpecView.jar"/>
-+          <srcfiles dir="${lib.dir}" includes="jspecview.app.jar"/>
-         </uptodate>
-         <uptodate targetfile="build/libjars.timestamp"
-                   srcfile="${appjars.dir}"/>
-@@ -396,7 +396,7 @@ all support for previous versions remove
-     <!-- unjar dest="${appjars.dir}" src="${lib.dir}/Acme.jar"/ -->
-     <unjar dest="${appjars.dir}" src="${lib.dir}/${itext.jar}"/>
-     <unjar dest="${appjars.dir}" src="${lib.dir}/${commons-cli.jar}"/>
--    <unjar dest="${appjars.dir}" src="${lib.dir}/JSpecView.jar"/>
-+    <unjar dest="${appjars.dir}" src="${lib.dir}/jspecview.app.jar"/>
-   	<delete dir="${appjars.dir}/org/jmol" />
-     <touch file="build/libjars.timestamp"/>
-   </target>
-@@ -1405,8 +1405,8 @@ all support for previous versions remove
-       <fileset dir="./appletweb">
-         <include name="README*.txt" />
-         <include name="Jmol*.js" />
--        <include name="JSpecViewApplet.jar" />
--        <include name="JSpecViewAppletSigned.jar" />
-+        <include name="jspecview.applet.jar" />
-+        <!--<include name="JSpecViewAppletSigned.jar" />-->
-       </fileset>
-     </copy>
- 
diff --git a/jmol-13.0.12-unbundle.patch b/jmol-13.0.12-unbundle.patch
deleted file mode 100644
index b4e473d..0000000
--- a/jmol-13.0.12-unbundle.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff -up jmol-13.0.12/build.xml.unbundle jmol-13.0.12/build.xml
---- jmol-13.0.12/build.xml.unbundle	2013-03-25 18:36:10.038001475 +0200
-+++ jmol-13.0.12/build.xml	2013-03-25 18:36:35.165238684 +0200
-@@ -74,6 +74,8 @@
-   <path id="project.class.path">
-     <fileset dir="${lib.dir}">
-       <include name="*.jar" />
-+      <include name="${vecmath.jar}" />
-+      <include name="${itext.jar}" />
-     </fileset>
-   </path>
-   
-@@ -391,12 +393,6 @@ all support for previous versions remove
-   <target name="libjars" id="libjars" depends="check.libjars" unless="libjars.uptodate">
-     <delete file="build/libjars.timestamp"/>
-     <mkdir dir="${appjars.dir}"/>
--    <unjar dest="${appjars.dir}" src="${lib.dir}/${vecmath.jar}"/>
--    <unjar dest="${appjars.dir}" src="${lib.dir}/${naga.jar}"/>
--    <!-- unjar dest="${appjars.dir}" src="${lib.dir}/Acme.jar"/ -->
--    <unjar dest="${appjars.dir}" src="${lib.dir}/${itext.jar}"/>
--    <unjar dest="${appjars.dir}" src="${lib.dir}/${commons-cli.jar}"/>
--    <unjar dest="${appjars.dir}" src="${lib.dir}/jspecview.app.jar"/>
-   	<delete dir="${appjars.dir}/org/jmol" />
-     <touch file="build/libjars.timestamp"/>
-   </target>
-@@ -568,35 +564,6 @@ all support for previous versions remove
-       </fileset>
-     </copy>
- 
--    <unjar dest="${appletjars.dir}" src="${lib.dir}/${vecmath.jar}">
--      <patternset>
--        <include name="**/Point3f.class"/>
--        <include name="**/Vector3f.class"/>
--        <include name="**/Matrix3f.class"/>
--        <include name="**/Matrix4f.class"/>
--        <include name="**/AxisAngle4f.class"/>
--        <include name="**/Quat4f.class"/>
--        <include name="**/Point3i.class"/>
--        <!-- the following are dependencies of the classes above -->
--        <include name="**/Tuple3i.class"/>
--        <include name="**/Tuple3f.class"/>
--        <include name="**/Tuple4f.class"/>
--        <include name="**/Vector4f.class"/>
--        <include name="**/Tuple3d.class"/>
--        <include name="**/Tuple4d.class"/>
--        <include name="**/Vector3d.class"/>
--        <include name="**/Quat4d.class"/>
--        <include name="**/Point4f.class"/>
--        <include name="**/Point3d.class"/>
--        <include name="**/Point4d.class"/>
--        <include name="**/Tuple2d.class"/>
--        <include name="**/Point2d.class"/>
--        <include name="**/Matrix3d.class"/>
--        <include name="**/Matrix4d.class"/>
--        <include name="**/AxisAngle4d.class"/>
--        <include name="**/SingularMatrixException.class"/>
--      </patternset>
--    </unjar>
-     <touch file="build/appletjars.timestamp"/>
-   </target>
- 
diff --git a/jmol-13.2.3-dontsign.patch b/jmol-13.2.3-dontsign.patch
new file mode 100644
index 0000000..53e675a
--- /dev/null
+++ b/jmol-13.2.3-dontsign.patch
@@ -0,0 +1,38 @@
+diff -up jmol-13.2.3/build.xml.nosign jmol-13.2.3/build.xml
+--- jmol-13.2.3/build.xml.nosign	2013-08-10 20:39:52.239445678 +0300
++++ jmol-13.2.3/build.xml	2013-08-10 20:41:05.407487719 +0300
+@@ -442,13 +442,14 @@ all support for previous versions remove
+       <fileset dir="${appjars.dir}" includes="**/*"/>
+       <fileset dir="src/org/jmol/translation/Jmol" includes="Messages*.class"/>
+     </jar>
+-    <signjar jar="${jmol.build.dir}/JmolUnsigned.jar"
++    
++    <!--<signjar jar="${jmol.build.dir}/JmolUnsigned.jar"
+              signedjar="${jmol.build.dir}/Jmol.jar"
+              keystore="selfSignedCertificate/selfSignedCertificate.store"
+-             storepass="selfSignedCertificate" alias="selfSignedCertificate" />
++             storepass="selfSignedCertificate" alias="selfSignedCertificate" />-->
+     <!-- to verify that a .jar file is signed: jarsigner -verify foo.jar -->
+   	
+-    <delete file="${jmol.build.dir}/JmolUnsigned.jar"/>
++    <!--    <delete file="${jmol.build.dir}/JmolUnsigned.jar"/> -->
+     <jar destfile="${jmol.build.dir}/JmolUnsignedF.jar"
+          manifest="manifest/applicationData.txt">
+       <fileset dir="${classes.dir}" >
+@@ -474,13 +475,13 @@ all support for previous versions remove
+       <fileset dir="${appjars.dir}" includes="**/cli/** **/naga/**" />
+       <fileset dir="src/org/jmol/translation/Jmol" includes="Messages*.class"/>
+     </jar>
+-    <signjar jar="${jmol.build.dir}/JmolUnsignedF.jar"
++    <!--<signjar jar="${jmol.build.dir}/JmolUnsignedF.jar"
+              signedjar="${jmol.build.dir}/JmolData.jar"
+              keystore="selfSignedCertificate/selfSignedCertificate.store"
+-             storepass="selfSignedCertificate" alias="selfSignedCertificate" />
++             storepass="selfSignedCertificate" alias="selfSignedCertificate" />-->
+     <!-- to verify that a .jar file is signed: jarsigner -verify foo.jar -->
+ 
+-  	<delete file="${jmol.build.dir}/JmolUnsignedF.jar"/>
++    <!--<delete file="${jmol.build.dir}/JmolUnsignedF.jar"/>-->
+     <copy todir="${jmol.build.dir}">
+       <fileset dir=".">
+         <include name="jmol" />
diff --git a/jmol-13.2.3-fedorabuild.patch b/jmol-13.2.3-fedorabuild.patch
new file mode 100644
index 0000000..96ec850
--- /dev/null
+++ b/jmol-13.2.3-fedorabuild.patch
@@ -0,0 +1,44 @@
+diff -up jmol-13.2.3/build.xml.fedorabuild jmol-13.2.3/build.xml
+--- jmol-13.2.3/build.xml.fedorabuild	2013-07-29 07:57:17.000000000 +0300
++++ jmol-13.2.3/build.xml	2013-08-10 20:37:41.715938271 +0300
+@@ -48,7 +48,7 @@
+   <property name="jvxl_version" value="0.1" />
+ 
+   <property name="tests.source.dir" value="source-tests" />
+-  <property name="lib.dir" value="jars" />
++  <property name="lib.dir" value="/usr/share/java" />
+   <property name="plugin.dir" value="plugin-jars" />
+   <property name="appjars.dir" value="build/appjars" />
+   <property name="classes.dir" value="build/classes" />
+@@ -63,10 +63,9 @@
+   <property name="jmol.build.dir" value="build" />
+   <property name="docbook-xsl" value="docbook-xsl-1.76.1" />
+   <property name="docbook-xml" value="docbook-xml-4.4" />
+-  <!--property name="vecmath.jar" value="vecmath1.2-1.14.jar" / -->
+-  <property name="naga.jar" value="naga-3_0.jar" />
+-  <property name="itext.jar" value="itext-1.4.5.jar" />
+-  <property name="commons-cli.jar" value="commons-cli-1.0.jar" />
++  <property name="naga.jar" value="naga.jar" />
++  <property name="itext.jar" value="itext.jar" />
++  <property name="commons-cli.jar" value="commons-cli.jar" />
+   <property name="saxon.jar" value="saxon.jar" />
+   <property name="saxon.main" value="com.icl.saxon.StyleSheet" />
+ 
+@@ -376,7 +375,7 @@ all support for previous versions remove
+           <!-- srcfiles dir="${lib.dir}" includes="Acme.jar"/ -->
+           <srcfiles dir="${lib.dir}" includes="${itext.jar}"/>
+           <srcfiles dir="${lib.dir}" includes="${commons-cli.jar}"/>
+-          <srcfiles dir="${lib.dir}" includes="JSpecView.jar"/>
++          <srcfiles dir="${lib.dir}" includes="jspecview.applet.jar"/>
+         </uptodate>
+         <uptodate targetfile="build/libjars.timestamp"
+                   srcfile="${appjars.dir}"/>
+@@ -409,7 +408,7 @@ all support for previous versions remove
+     <!-- unjar dest="${appjars.dir}" src="${lib.dir}/Acme.jar"/ -->
+     <unjar dest="${appjars.dir}" src="${lib.dir}/${itext.jar}"/>
+     <unjar dest="${appjars.dir}" src="${lib.dir}/${commons-cli.jar}"/>
+-    <unjar dest="${appjars.dir}" src="${lib.dir}/JSpecView.jar"/>
++    <unjar dest="${appjars.dir}" src="${lib.dir}/jspecview.applet.jar"/>
+   	<delete dir="${appjars.dir}/org/jmol" />
+     <touch file="build/libjars.timestamp"/>
+   </target>
diff --git a/jmol-13.2.3-unbundle.patch b/jmol-13.2.3-unbundle.patch
new file mode 100644
index 0000000..a5b7804
--- /dev/null
+++ b/jmol-13.2.3-unbundle.patch
@@ -0,0 +1,27 @@
+diff -up jmol-13.2.3/build.xml.unbundle jmol-13.2.3/build.xml
+--- jmol-13.2.3/build.xml.unbundle	2013-08-10 20:38:15.427036218 +0300
++++ jmol-13.2.3/build.xml	2013-08-10 20:39:20.082306100 +0300
+@@ -82,6 +82,8 @@
+   <path id="project.class.path">
+     <fileset dir="${lib.dir}">
+       <include name="*.jar" />
++      <include name="${vecmath.jar}" />
++      <include name="${itext.jar}" />
+     </fileset>
+   </path>
+   
+@@ -403,13 +405,7 @@ all support for previous versions remove
+   <target name="libjars" id="libjars" depends="check.libjars" unless="libjars.uptodate">
+     <delete file="build/libjars.timestamp"/>
+     <mkdir dir="${appjars.dir}"/>
+-    <!-- unjar dest="${appjars.dir}" src="${lib.dir}/${vecmath.jar}"/ -->
+-    <unjar dest="${appjars.dir}" src="${lib.dir}/${naga.jar}"/>
+-    <!-- unjar dest="${appjars.dir}" src="${lib.dir}/Acme.jar"/ -->
+-    <unjar dest="${appjars.dir}" src="${lib.dir}/${itext.jar}"/>
+-    <unjar dest="${appjars.dir}" src="${lib.dir}/${commons-cli.jar}"/>
+-    <unjar dest="${appjars.dir}" src="${lib.dir}/jspecview.applet.jar"/>
+-  	<delete dir="${appjars.dir}/org/jmol" />
++   	<delete dir="${appjars.dir}/org/jmol" />
+     <touch file="build/libjars.timestamp"/>
+   </target>
+ 
diff --git a/jmol.spec b/jmol.spec
index 1c15f6b..28beb27 100644
--- a/jmol.spec
+++ b/jmol.spec
@@ -1,6 +1,6 @@
 Name:        jmol
-Version:     13.0.15
-Release:     2%{?dist}
+Version:     13.2.3
+Release:     1%{?dist}
 Summary:     An open-source Java viewer for chemical structures in 3D
 Group:       Applications/Engineering
 # most is LGPLv2+, src/com/obrador is combination of IJG and BSD
@@ -12,11 +12,11 @@ Source0:     http://downloads.sourceforge.net/%{name}/Jmol-%{version}-full.tar.g
 # Image available at "http://wiki.jmol.org:81/index.php/Image:Jmol_icon_128.png"
 Source1:     Jmol_icon_128.png
 # Patch to get Jmol to build in Fedora (location of JAR files)
-Patch0:      jmol-13.0.12-fedorabuild.patch
+Patch0:      jmol-13.2.3-fedorabuild.patch
 # Unbundle bundled classes from jars
-Patch1:      jmol-13.0.12-unbundle.patch
+Patch1:      jmol-13.2.3-unbundle.patch
 # Don't try to sign jars
-Patch2:      jmol-13.0.12-dontsign.patch
+Patch2:      jmol-13.2.3-dontsign.patch
 # Don't ignore the system classpath
 Patch3:      jmol-12.0.48-classpath.patch
 
@@ -32,8 +32,6 @@ BuildRequires:    java-devel >= 1:1.6.0
 BuildRequires:    jpackage-utils
 BuildRequires:	  jspecview
 BuildRequires:	  naga
-# For javax.vecmath
-BuildRequires:    vecmath
 
 %if 0%{?fedora} > 14
 # In newer releases some of the necessary Java classes are
@@ -167,6 +165,9 @@ rm -rf %{buildroot}
 %doc build/doc/*
 
 %changelog
+* Sat Aug 10 2013 Susi Lehtola <jussilehtola@fedoraproject.org> - 13.2.3-1
+- Update to 13.2.3.
+
 * Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 13.0.15-2
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
 
diff --git a/sources b/sources
index 2e55e6d..791c2f1 100644
--- a/sources
+++ b/sources
@@ -1,2 +1,2 @@
 75268c66c9afac86a59d6348745dd1e4  Jmol_icon_128.png
-8798cd62f04cd3d699225b8fe84017f3  Jmol-13.0.15-full.tar.gz
+22056684533d73f879c98f2b1534bb35  Jmol-13.2.3-full.tar.gz