[jmol] Update to 13.0.15.
Susi Lehtola
jussilehtola at fedoraproject.org
Tue May 14 13:06:45 UTC 2013
commit 415bcd7754c9d387d326d99fc850158497a8c934
Author: Susi Lehtola <jussilehtola at fedoraproject.org>
Date: Tue May 14 16:06:42 2013 +0300
Update to 13.0.15.
.gitignore | 1 +
jmol-12.0.41-dontsign.patch | 132 --------------------
jmol-12.0.41-fedorabuild.patch | 25 ----
jmol-12.0.48-javadoc-encoding.patch | 24 ----
jmol-13.0.12-dontsign.patch | 38 ++++++
jmol-13.0.12-fedorabuild.patch | 56 ++++++++
...8-unbundle.patch => jmol-13.0.12-unbundle.patch | 29 ++---
jmol.spec | 98 ++++++++-------
sources | 3 +-
9 files changed, 157 insertions(+), 249 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index 91fef5b..453304d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@ Jmol_icon_128.png
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
diff --git a/jmol-13.0.12-dontsign.patch b/jmol-13.0.12-dontsign.patch
new file mode 100644
index 0000000..0917b9c
--- /dev/null
+++ b/jmol-13.0.12-dontsign.patch
@@ -0,0 +1,38 @@
+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="${jmol.build.dir}">
+ <fileset dir=".">
+ <include name="jmol" />
diff --git a/jmol-13.0.12-fedorabuild.patch b/jmol-13.0.12-fedorabuild.patch
new file mode 100644
index 0000000..3c89f86
--- /dev/null
+++ b/jmol-13.0.12-fedorabuild.patch
@@ -0,0 +1,56 @@
+diff -up jmol-13.0.12/build.xml.orig jmol-13.0.12/build.xml
+--- jmol-13.0.12/build.xml.orig 2013-01-25 09:03:22.000000000 +0200
++++ jmol-13.0.12/build.xml 2013-03-25 18:35:58.477352422 +0200
+@@ -40,7 +40,7 @@
+ <property name="jvxl_version" value="0.1" />
+
+ <property name="tests.source.dir" value="source-tests" />
+- <property name="lib.dir" value="jars" />
++ <property name="lib.dir" value="/usr/share/java" />
+ <property name="plugin.dir" value="plugin-jars" />
+ <property name="appjars.dir" value="build/appjars" />
+ <property name="classes.dir" value="build/classes" />
+@@ -54,10 +54,10 @@
+ <property name="jmol.build.dir" value="build" />
+ <property name="docbook-xsl" value="docbook-xsl-1.76.1" />
+ <property name="docbook-xml" value="docbook-xml-4.4" />
+- <property name="vecmath.jar" value="vecmath1.2-1.14.jar" />
+- <property name="naga.jar" value="naga-3_0.jar" />
+- <property name="itext.jar" value="itext-1.4.5.jar" />
+- <property name="commons-cli.jar" value="commons-cli-1.0.jar" />
++ <property name="vecmath.jar" value="vecmath.jar" />
++ <property name="naga.jar" value="naga.jar" />
++ <property name="itext.jar" value="itext.jar" />
++ <property name="commons-cli.jar" value="commons-cli.jar" />
+ <property name="saxon.jar" value="saxon.jar" />
+ <property name="saxon.main" value="com.icl.saxon.StyleSheet" />
+
+@@ -363,7 +363,7 @@ all support for previous versions remove
+ <!-- srcfiles dir="${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-12.0.48-unbundle.patch b/jmol-13.0.12-unbundle.patch
similarity index 77%
rename from jmol-12.0.48-unbundle.patch
rename to jmol-13.0.12-unbundle.patch
index 7d9100f..b4e473d 100644
--- a/jmol-12.0.48-unbundle.patch
+++ b/jmol-13.0.12-unbundle.patch
@@ -1,17 +1,7 @@
-From 644a2cef2960a7151b0b53ef42082195179f446c Mon Sep 17 00:00:00 2001
-From: Stanislav Ochotnicky <sochotnicky at redhat.com>
-Date: Mon, 7 May 2012 15:48:19 +0200
-Subject: [PATCH 1/2] unbundle
-
----
- build.xml | 35 ++---------------------------------
- 1 files changed, 2 insertions(+), 33 deletions(-)
-
-diff --git a/build.xml b/build.xml
-index 543ab81..8e7aeeb 100644
---- a/build.xml
-+++ b/build.xml
-@@ -55,6 +55,8 @@
+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="${lib.dir}">
<include name="*.jar" />
@@ -20,18 +10,20 @@ index 543ab81..8e7aeeb 100644
</fileset>
</path>
-@@ -376,10 +378,6 @@ all support for previous versions removed
+@@ -391,12 +393,6 @@ all support for previous versions remove
<target name="libjars" id="libjars" depends="check.libjars" unless="libjars.uptodate">
<delete file="build/libjars.timestamp"/>
<mkdir dir="${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>
-
-@@ -539,35 +537,6 @@ all support for previous versions removed
+@@ -568,35 +564,6 @@ all support for previous versions remove
</fileset>
</copy>
@@ -67,6 +59,3 @@ index 543ab81..8e7aeeb 100644
<touch file="build/appletjars.timestamp"/>
</target>
---
-1.7.7.6
-
diff --git a/jmol.spec b/jmol.spec
index 83a4c85..7d4c04c 100644
--- a/jmol.spec
+++ b/jmol.spec
@@ -1,49 +1,49 @@
-Name: jmol
-Version: 12.0.48
-Release: 10%{?dist}
-Summary: An open-source Java viewer for chemical structures in 3D
-Group: Applications/Engineering
+Name: jmol
+Version: 13.0.15
+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
# src/org@/jmol/export/image is partially 2 clause BSD
-License: LGPLv2+ and IJG and BSD
-URL: http://jmol.sourceforge.net
-BuildArch: noarch
-Source0: http://downloads.sourceforge.net/%{name}/Jmol-%{version}-full.tar.gz
+License: LGPLv2+ and IJG and BSD
+URL: http://jmol.sourceforge.net
+BuildArch: noarch
+Source0: http://downloads.sourceforge.net/%{name}/Jmol-%{version}-full.tar.gz
# Image available at "http://wiki.jmol.org:81/index.php/Image:Jmol_icon_128.png"
-Source1: Jmol_icon_128.png
+Source1: Jmol_icon_128.png
# Patch to get Jmol to build in Fedora (location of JAR files)
-Patch0: jmol-12.0.41-fedorabuild.patch
+Patch0: jmol-13.0.12-fedorabuild.patch
# Unbundle bundled classes from jars
-Patch1: jmol-12.0.48-unbundle.patch
+Patch1: jmol-13.0.12-unbundle.patch
# Don't try to sign jars
-Patch2: jmol-12.0.41-dontsign.patch
+Patch2: jmol-13.0.12-dontsign.patch
# Don't ignore the system classpath
-Patch3: jmol-12.0.48-classpath.patch
-# Fix javadoc encoding problems by forcing utf-8
-Patch4: jmol-12.0.48-javadoc-encoding.patch
+Patch3: jmol-12.0.48-classpath.patch
-BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
-BuildRequires: ant, ant-contrib
-BuildRequires: desktop-file-utils
-BuildRequires: gettext-devel
-BuildRequires: itext
-BuildRequires: apache-commons-cli
-BuildRequires: java-devel >= 1:1.6.0
-BuildRequires: jpackage-utils
+BuildRequires: ant, ant-contrib
+BuildRequires: desktop-file-utils
+BuildRequires: gettext-devel
+BuildRequires: itext
+BuildRequires: apache-commons-cli
+BuildRequires: java-devel >= 1:1.6.0
+BuildRequires: jpackage-utils
+BuildRequires: jspecview
+BuildRequires: naga
# For javax.vecmath
-BuildRequires: vecmath
+BuildRequires: vecmath
%if 0%{?fedora} > 14
# In newer releases some of the necessary Java classes are
# in the browser plugin package
-BuildRequires: icedtea-web
-Requires: icedtea-web
+BuildRequires: icedtea-web
+Requires: icedtea-web
%endif
-Requires: java >= 1:1.6.0
-Requires: jpackage-utils
+Requires: java >= 1:1.6.0
+Requires: jpackage-utils
Requires: itext
Requires: vecmath
Requires: apache-commons-cli
@@ -54,19 +54,19 @@ and researchers in chemistry and biochemistry.
%package javadoc
-Summary: Java docs for %{name}
-Group: Documentation
-Requires: %{name} = %{version}-%{release}
-Requires: jpackage-utils
+Summary: Java docs for %{name}
+Group: Documentation
+Requires: %{name} = %{version}-%{release}
+Requires: jpackage-utils
%description javadoc
This package contains the API documentation for %{name}.
%package doc
-Summary: Documentation for %{name}
-Group: Documentation
-Requires: %{name} = %{version}-%{release}
+Summary: Documentation for %{name}
+Group: Documentation
+Requires: %{name} = %{version}-%{release}
%description doc
The documentation for %{name}.
@@ -78,7 +78,6 @@ The documentation for %{name}.
%patch1 -p1 -b .unbundle
%patch2 -p1 -b .nosign
%patch3 -p1 -b .classpath
-%patch4 -p1 -b .encoding
# Remove binaries
find -name '*.class' -exec rm -f '{}' \;
@@ -90,9 +89,9 @@ rm -f jars/*
find -name "*.txt" -exec chmod 644 {} \;
# Fix EOL encoding
for doc in README.txt COPYRIGHT.txt LICENSE.txt CHANGES.txt; do
- sed "s|\r||g" $doc > $doc.new && \
- touch -r $doc $doc.new && \
- mv $doc.new $doc
+sed "s|\r||g" $doc > $doc.new && \
+touch -r $doc $doc.new && \
+mv $doc.new $doc
done
@@ -114,10 +113,14 @@ export ANT_OPTS="-Dfile.encoding=utf-8"
%if 0%{?fedora} > 15
# Need to be able to find netscape.javascript.*classes
PLUGIN_JAR=%{_datadir}/icedtea-web/plugin.jar
-jar tf $PLUGIN_JAR | grep JSObject
-ant --execdebug -lib $PLUGIN_JAR doc main
+jar tf $PLUGIN_JAR | grep javascript/JSObject.class
+#ant --execdebug -lib $PLUGIN_JAR doc jar applet-jar
+
+ant --execdebug -lib $PLUGIN_JAR jar
+ant --execdebug -lib $PLUGIN_JAR applet-jar
+ant --execdebug -lib $PLUGIN_JAR doc
%else
-ant --execdebug doc main
+ant --execdebug doc jar applet-jar
%endif
%install
@@ -131,9 +134,9 @@ install -D -p -m 644 %{SOURCE1} %{buildroot}%{_datadir}/pixmaps/%{name}.png
# Install desktop file
desktop-file-install --dir=${RPM_BUILD_ROOT}%{_datadir}/applications \
%if (0%{?fedora} && 0%{?fedora} < 19) || ( 0%{?rhel} && 0%{?rhel} < 7)
- --vendor=fedora \
+--vendor=fedora \
%endif
- jmol.desktop
+jmol.desktop
# Javadoc files
mkdir -p %{buildroot}%{_javadocdir}/%{name}
@@ -164,6 +167,9 @@ rm -rf %{buildroot}
%doc build/doc/*
%changelog
+* Tue May 14 2013 Susi Lehtola <jussilehtola at fedoraproject.org> - 13.0.15-1
+- Update to 13.0.15.
+
* Wed Mar 6 2013 Toshio Kuratomi <toshio at fedoraproject.org> - 12.0.48-10
- Remove vendor prefix from desktop files in F19+ https://fedorahosted.org/fesco/ticket/1077
@@ -241,7 +247,7 @@ rm -rf %{buildroot}
* Wed Dec 23 2009 Jussi Lehtola <jussilehtola at fedoraproject.org> - 11.8.14-1
- Build from stable release tarballs works now, switch to using stable
- releases.
+releases.
- Update to 11.8.14.
* Fri Oct 02 2009 Jussi Lehtola <jussilehtola at fedoraproject.org> - 11.8-1.11581
diff --git a/sources b/sources
index 8601714..7031a2d 100644
--- a/sources
+++ b/sources
@@ -1,2 +1 @@
-75268c66c9afac86a59d6348745dd1e4 Jmol_icon_128.png
-991f7b81dc1dce91a6dedec4ffb012fe Jmol-12.0.48-full.tar.gz
+8798cd62f04cd3d699225b8fe84017f3 Jmol-13.0.15-full.tar.gz
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