Latest version

(Portage version: 2.1.10.63/cvs/Linux x86_64)

3 files changed, 457 insertions, 1 deletions

diff --git a/sci-chemistry/jmol/ChangeLog b/sci-chemistry/jmol/ChangeLog
index 179e1b816284..cf56564811b3 100644
--- a/sci-chemistry/jmol/ChangeLog
+++ b/sci-chemistry/jmol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/jmol
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/jmol/ChangeLog,v 1.12 2012/02/15 14:14:10 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/jmol/ChangeLog,v 1.13 2012/05/31 21:00:54 je_fro Exp $
+
+*jmol-12.2.27 (31 May 2012)
+
+  31 May 2012; Jeff Gardner <je_fro@gentoo.org> +jmol-12.2.27.ebuild,
+  +files/jmol-12.2.27-nointl.patch:
+  Latest version
 
   15 Feb 2012; Kacper Kowalik <xarthisius@gentoo.org> jmol-11.0.3-r1.ebuild:
   Fix SRC_URI
diff --git a/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
new file mode 100644
index 000000000000..0a43faaf653d
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
@@ -0,0 +1,330 @@
+--- orig-build.xml	2012-05-31 13:42:43.943062427 -0500
++++ build.xml	2012-05-31 14:01:01.691982062 -0500
+@@ -52,8 +52,6 @@
+ 

+   <property file="proxy.properties" />

+ 

+-  <import file="tools/build-i18n.xml"/>

+-

+   <path id="project.class.path">

+     <fileset dir="${lib.dir}">

+       <include name="*.jar" />

+@@ -111,10 +109,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -124,14 +118,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />

+-        </uptodate>

+       </and>

+     </condition>

+     

+@@ -141,14 +127,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolDevelopersGuide.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolDevelopersGuide_fr.docbook.xml"/>

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolDevelopersGuide_de.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -158,14 +136,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolAppletGuide_de.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolAppletGuide_de.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -388,17 +358,12 @@
+   </target>

+ 

+   <target name="jar" id="jar"

+-          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">

++          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">

+     <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >

+       <fileset dir="build/doc/JmolUserGuide">

+         <include name="**/*.html" />

+       </fileset>

+     </copy>

+-    <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >

+-      <fileset dir="build/doc/JmolUserGuide_fr">

+-        <include name="**/*.html" />

+-      </fileset>

+-    </copy>

+     <copy todir="${classes.dir}/org/openscience/jmol/Data" >

+       <fileset dir="build/doc/JmolHistory">

+         <include name="**/*.html" />

+@@ -603,18 +568,6 @@
+       <fileset dir="${appletjars.dir}" includes="**/*"/>

+     </jar>

+ 

+-    <for list="${all.JmolApplet.languages}" delimiter=","

+-         param="current.Jmol.language">

+-      <sequential>

+-        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

+-             manifest="manifest/applet_i18n.txt" >

+-          <fileset dir="${applet.classes.dir}">

+-            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />

+-          </fileset>

+-        </jar>

+-      </sequential>

+-    </for>

+-

+     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">

+       <fileset dir="${applet.classes.dir}">

+         <include name="org/jmol/minimize/**" />

+@@ -729,7 +682,6 @@
+         <include name="org/jmol/constant/**" />

+         <include name="org/jmol/g3d/**" />

+         <include name="org/jmol/geodesic/**" />

+-        <include name="org/jmol/i18n/**" />

+         <include name="org/jmol/modelset/**" />

+         <include name="org/jmol/script/**" />

+         <include name="org/jmol/shape/**" />

+@@ -755,7 +707,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />

+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />

+       </indexjars>

+     </jar>

+     <!-- changes to this must be replicated below for the signed applet -->

+@@ -868,16 +819,6 @@
+              keystore="selfSignedCertificate/selfSignedCertificate.store"

+              storepass="selfSignedCertificate" alias="selfSignedCertificate" />

+ 

+-    <for list="${all.JmolApplet.languages}" delimiter=","

+-         param="current.Jmol.language">

+-      <sequential>

+-      	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

+-                 signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"

+-                 keystore="selfSignedCertificate/selfSignedCertificate.store"

+-                 storepass="selfSignedCertificate" alias="selfSignedCertificate" />

+-      </sequential>

+-    </for>

+-

+     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->

+     <!-- this one must be treated specially because of jar indexing

+          we cannot simply rename the jar file, because the index has

+@@ -905,7 +846,6 @@
+ 		<include name="org/jmol/shape/**" />

+ 		<include name="org/jmol/viewer/**" />

+ 		<include name="org/jmol/util/**" />

+-		<include name="org/jmol/i18n/**" />

+       </fileset>    	

+       <indexjars>

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Console.jar" />

+@@ -924,7 +864,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />

+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />

+       </indexjars>

+     </jar>

+     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"

+@@ -963,18 +902,6 @@
+       </fileset>

+     </jar>

+ 

+-    <for list="${all.JmolApplet.languages}" delimiter=","

+-         param="current.Jmol.language">

+-      <sequential>

+-        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

+-             manifest="manifest/applet_i18n.txt" >

+-          <fileset dir="${applet.classes.dir}">

+-            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />

+-          </fileset>

+-        </jar>

+-      </sequential>

+-    </for>

+-

+     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">

+       <fileset dir="${applet.classes.dir}">

+         <include name="org/jmol/minimize/**" />

+@@ -1088,7 +1015,6 @@
+         <include name="org/jmol/constant/**" />

+         <include name="org/jmol/g3d/**" />

+         <include name="org/jmol/geodesic/**" />

+-        <include name="org/jmol/i18n/**" />

+         <include name="org/jmol/modelset/**" />

+         <include name="org/jmol/script/**" />

+         <include name="org/jmol/shape/**" />

+@@ -1114,7 +1040,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />

+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />

+       </indexjars>

+     </jar>

+     <!-- changes to this must be replicated below for the signed applet -->

+@@ -1123,7 +1048,7 @@
+   </target>

+ 

+   <target name="dist" id="dist"

+-          depends="doc,main-i18n,main,signed-applet">

++          depends="doc,main,signed-applet">

+     <!-- first build binary distribution -->

+     <delete dir="build/dist/jmol-${version}"/>

+     <mkdir dir="build/dist/jmol-${version}"/>

+@@ -1183,7 +1108,6 @@
+       <fileset dir=".">

+         <include name="applet.classes" />

+         <include name="build.xml" />

+-        <include name="build-i18n.xml" />

+       </fileset>

+     </copy>

+ 

+@@ -1278,7 +1202,6 @@
+       <fileset dir=".">

+         <include name="apisio.classes" />

+         <include name="build.xml" />

+-        <include name="build-i18n.xml" />

+       </fileset>

+     </copy>

+ 

+@@ -1374,7 +1297,7 @@
+   <target name="xclean" id="xclean">

+   </target>

+ 

+-  <target name="spotless" id="spotless" depends="clean,spotless-i18n">

++  <target name="spotless" id="spotless" depends="clean">

+     <delete dir="build"/>

+     <delete dir="${javadoc.dir}"/>

+     <delete dir="packaging/rpm/dist"/>

+@@ -1438,16 +1361,6 @@
+       <arg value="../../../doc/source/JmolGuide.docbook.xml" />

+       <arg value="../../${docbook-xsl}/html/chunk.xsl" />

+     </java>

+-    <echo message="Generating user's guide (fr)" />

+-    <mkdir dir="build/doc/JmolUserGuide_fr" />

+-    <java fork="true" dir="build/doc/JmolUserGuide_fr"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <jvmarg value="${proxyHost}" />

+-      <jvmarg value="${proxyPort}" />

+-      <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />

+-      <arg value="../../${docbook-xsl}/html/chunk.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolHistory" id="jmolHistory"

+@@ -1462,26 +1375,6 @@
+       <arg value="../../../doc/source/JmolHistory.xml" />

+       <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+     </java>

+-    <echo message="Generating history of changes (fr)" />

+-    <java fork="true" dir="build/doc/JmolHistory"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="ChangeLog_fr.html" />

+-      <arg value="../../../doc/source/JmolHistory_fr.xml" />

+-      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+-      <arg value="lang=fr" />

+-    </java>

+-    <echo message="Generating history of changes (nl)" />

+-    <java fork="true" dir="build/doc/JmolHistory"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="ChangeLog_nl.html" />

+-      <arg value="../../../doc/source/JmolHistory_nl.xml" />

+-      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+-      <arg value="lang=nl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"

+@@ -1495,24 +1388,6 @@
+       <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />

+       <arg value="../${docbook-xsl}/html/docbook.xsl" />

+     </java>

+-    <echo message="Generating developer's guide (fr)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolDevelopersGuide_fr.html" />

+-      <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+-    <echo message="Generating developer's guide (de)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolDevelopersGuide_de.html" />

+-      <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"

+@@ -1526,24 +1401,6 @@
+       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />

+       <arg value="../${docbook-xsl}/html/docbook.xsl" />

+     </java>

+-    <echo message="Generating applet guide (fr)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolAppletGuide_fr.html" />

+-      <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+-    <echo message="Generating applet guide (de)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolAppletGuide_de.html" />

+-      <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="test" id="test" depends="main,compile-tests">

+@@ -1575,12 +1432,4 @@
+     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />

+   </target>

+ 

+-  <!-- i18n stuff -->

+-  <target name="main-i18n" depends="classes">

+-    <ant antfile="tools/build-i18n.xml" target="main-i18n"/>

+-  </target>

+-  <target name="spotless-i18n">

+-    <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>

+-  </target>

+-

+ </project>

diff --git a/sci-chemistry/jmol/jmol-12.2.27.ebuild b/sci-chemistry/jmol/jmol-12.2.27.ebuild
new file mode 100644
index 000000000000..6700142545d6
--- /dev/null
+++ b/sci-chemistry/jmol/jmol-12.2.27.ebuild
@@ -0,0 +1,120 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/jmol/jmol-12.2.27.ebuild,v 1.1 2012/05/31 21:00:54 je_fro Exp $
+
+EAPI=1
+WEBAPP_OPTIONAL="yes"
+
+inherit eutils webapp java-pkg-2 java-ant-2
+
+MY_P="Jmol"
+
+DESCRIPTION="Jmol is a java molecular viever for 3-D chemical structures."
+SRC_URI="
+	mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz
+	http://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar"
+
+HOMEPAGE="http://jmol.sourceforge.net/"
+KEYWORDS="~x86 ~amd64"
+LICENSE="LGPL-2.1"
+
+IUSE="client-only vhosts"
+
+WEBAPP_MANUAL_SLOT="yes"
+SLOT="0"
+
+COMMON_DEP="dev-java/commons-cli
+	dev-java/itext:0
+	sci-libs/jmol-acme
+	sci-libs/vecmath-objectclub
+	sci-libs/naga"
+RDEPEND=">=virtual/jre-1.5
+	${COMMON_DEP}"
+DEPEND=">=virtual/jdk-1.5
+	dev-java/saxon:6.5
+	!client-only? ( ${WEBAPP_DEPEND} )
+	${COMMON_DEP}"
+
+pkg_setup() {
+
+	use client-only || webapp_pkg_setup
+	java-pkg-2_pkg_setup
+}
+
+src_unpack() {
+
+	unpack ${A}
+	cd "${S}"
+
+	epatch "${FILESDIR}"/${P}-nointl.patch
+
+	rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die
+	cd "${S}/jars"
+
+# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along.
+	if use amd64; then
+		mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar."
+		rm -v *.jar *.tar.gz || die "Failed to remove jars."
+		mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar."
+	fi
+
+	java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar
+	java-pkg_jar-from itext iText.jar itext-1.4.5.jar
+	java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar
+	java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar
+	java-pkg_jar-from naga
+	java-pkg_jar-from saxon-6.5 saxon.jar
+
+	mkdir -p "${S}/build/appjars" || die
+}
+
+src_compile() {
+	# prevent absorbing dep's classes
+	eant -Dlibjars.uptodate=true main
+}
+
+src_install() {
+
+	java-pkg_dojar build/Jmol.jar
+	dohtml -r  build/doc/* || die "Failed to install html docs."
+	dodoc *.txt doc/*license* || die "Failed to install licenses."
+
+	java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \
+		--java_args "-Xmx512m"
+
+	if ! use client-only ; then
+		webapp_src_preinst || die "Failed webapp_src_preinst."
+		cmd="cp Jmol.js build/Jmol.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp build/JmolApplet*.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp applet.classes "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp -r build/classes/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp -r build/appletjars/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp "${FILESDIR}"/caffeine.xyz "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp "${FILESDIR}"/index.html "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+
+		webapp_src_install || die "Failed running webapp_src_install"
+	fi
+}
+
+pkg_postinst() {
+
+	if ! use client-only ; then
+		webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+	fi
+
+}
+
+pkg_prerm() {
+
+	if ! use client-only ; then
+		webapp_pkg_prerm || die "webapp_pkg_prerm failed"
+	fi
+
+}