From mboxrd@z Thu Jan  1 00:00:00 1970
Return-Path: <gentoo-commits+bounces-617382-garchives=archives.gentoo.org@lists.gentoo.org>
Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80])
	by finch.gentoo.org (Postfix) with ESMTP id 892661381F3
	for <garchives@archives.gentoo.org>; Fri,  9 Aug 2013 11:51:07 +0000 (UTC)
Received: from pigeon.gentoo.org (localhost [127.0.0.1])
	by pigeon.gentoo.org (Postfix) with SMTP id C8DAEE0C38;
	Fri,  9 Aug 2013 11:51:03 +0000 (UTC)
Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183])
	(using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits))
	(No client certificate requested)
	by pigeon.gentoo.org (Postfix) with ESMTPS id 428A0E0C38
	for <gentoo-commits@lists.gentoo.org>; Fri,  9 Aug 2013 11:51:03 +0000 (UTC)
Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163])
	(using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits))
	(No client certificate requested)
	by smtp.gentoo.org (Postfix) with ESMTPS id 2CA2B33EBA0
	for <gentoo-commits@lists.gentoo.org>; Fri,  9 Aug 2013 11:51:02 +0000 (UTC)
Received: from localhost.localdomain (localhost [127.0.0.1])
	by hornbill.gentoo.org (Postfix) with ESMTP id AA1E9E468F
	for <gentoo-commits@lists.gentoo.org>; Fri,  9 Aug 2013 11:51:00 +0000 (UTC)
From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=UTF-8
Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" <jlec@gentoo.org>
Message-ID: <1376049047.73ebe4639b3d167031fcd2ec270c72a9cc6b8f1d.jlec@gentoo>
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/jmol/, sci-chemistry/jmol/files/, ...
X-VCS-Repository: proj/sci
X-VCS-Files: sci-chemistry/jmol/ChangeLog sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch sci-chemistry/jmol/files/caffeine.xyz sci-chemistry/jmol/files/index.html sci-chemistry/jmol/files/selfSignedCertificate.store sci-chemistry/jmol/jmol-12.0.45-r1.ebuild sci-chemistry/jmol/metadata.xml
X-VCS-Directories: sci-chemistry/jmol/ sci-chemistry/jmol/files/ sci-chemistry/jmol/files/12.0.45/
X-VCS-Committer: jlec
X-VCS-Committer-Name: Justin Lecher
X-VCS-Revision: 73ebe4639b3d167031fcd2ec270c72a9cc6b8f1d
X-VCS-Branch: master
Date: Fri,  9 Aug 2013 11:51:00 +0000 (UTC)
Precedence: bulk
List-Post: <mailto:gentoo-commits@lists.gentoo.org>
List-Help: <mailto:gentoo-commits+help@lists.gentoo.org>
List-Unsubscribe: <mailto:gentoo-commits+unsubscribe@lists.gentoo.org>
List-Subscribe: <mailto:gentoo-commits+subscribe@lists.gentoo.org>
List-Id: Gentoo Linux mail <gentoo-commits.gentoo.org>
X-BeenThere: gentoo-commits@lists.gentoo.org
X-Archives-Salt: 5f7823db-966a-42b2-9c07-6fe40fc04de7
X-Archives-Hash: 87b5d3a15d19204887daac06032528d1

commit:     73ebe4639b3d167031fcd2ec270c72a9cc6b8f1d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Aug  9 11:50:47 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Aug  9 11:50:47 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=73ebe463

newer version in tree

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 sci-chemistry/jmol/ChangeLog                       |  54 ----
 .../jmol/files/12.0.45/jmol-manifest.patch         |  96 -------
 sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch | 313 ---------------------
 sci-chemistry/jmol/files/caffeine.xyz              |  26 --
 sci-chemistry/jmol/files/index.html                |  14 -
 .../jmol/files/selfSignedCertificate.store         | Bin 1516 -> 0 bytes
 sci-chemistry/jmol/jmol-12.0.45-r1.ebuild          | 122 --------
 sci-chemistry/jmol/metadata.xml                    |  13 -
 8 files changed, 638 deletions(-)

diff --git a/sci-chemistry/jmol/ChangeLog b/sci-chemistry/jmol/ChangeLog
deleted file mode 100644
index 6988a07..0000000
--- a/sci-chemistry/jmol/ChangeLog
+++ /dev/null
@@ -1,54 +0,0 @@
-# ChangeLog for sci-chemistry/jmol
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  29 Mar 2011; Jeff Gardner <je_fro@gentoo.org> jmol-12.0.34.ebuild:
-  Add ~amd64 for testing by others.
-
-*jmol-11.6 (23 Apr 2009)
-
-  23 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/jmol-11.6-manifest.patch, +files/jmol-11.6-nointl.patch,
-  +files/caffeine.xyz, +files/index.html,
-  +files/selfSignedCertificate.store, +metadata.xml, +jmol-11.6.ebuild:
-  version bump
-
-  05 Oct 2008; Petteri Räty <betelgeuse@gentoo.org> jmol-11.0.3-r1.ebuild:
-  Add slot deps.
-
-  06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
-  Add USE flag description to metadata wrt GLEP 56.
-
-  15 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>;
-  jmol-11.0.3-r1.ebuild:
-  Fix conditional webapp to not pull in webapp-config when it's unneeded.
-
-  31 Dec 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
-  Fixing my email address.
-
-  02 Sep 2007; <je_fro@gentoo.org> jmol-11.0.3-r1.ebuild:
-  Fix conditional code moving netscape.jar wrt bug #191032
-
-  05 Jul 2007; Jeff Gardner <je_fro@gentoo.org> jmol-11.0.3-r1.ebuild:
-  Protecting netscape.jar from removal on amd64.
-
-  22 Jun 2007; Jeff Gardner <je_fro@gentoo.org> jmol-11.0.3-r1.ebuild:
-  Removing ~amd64 for jmol-11.0.3-r1 because the bundled netscape.jar is still
-  required on this arch.
-
-*jmol-11.0.3-r1 (22 Jun 2007)
-
-  22 Jun 2007; Vlastimil Babka <caster@gentoo.org> jmol-11.0.3.ebuild,
-  +jmol-11.0.3-r1.ebuild:
-  Revbump for java-related fixes - install jars we've built and not the
-  bundled ones, don't absorb dependencies' classes, depend only on what's
-  actually needed, use java dolauncher instead of supplied one. Keyword ~x86.
-
-*jmol-11.0.3 (15 Jun 2007)
-
-  15 Jun 2007; Jeff Gardner <je_fro@gentoo.org>
-  +files/jmol-11.0.3-manifest.patch, +files/jmol-11.0.3-nointl.patch,
-  +files/caffeine.xyz, +files/index.html,
-  +files/selfSignedCertificate.store, +jmol-11.0.3.ebuild:
-  Initial import of jmol-11.0.3.
-

diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
deleted file mode 100644
index 3b43c21..0000000
--- a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt
---- jmol-11.0.3-orig/manifest/applet0.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet0.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,6 @@
-+Main-Class: JmolApplet
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt
---- jmol-11.0.3-orig/manifest/applet1.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet1.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,6 @@
-+Name: org/jmol/api/
-+Sealed: false
-+
-+Name: org/jmol/applet/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt
---- jmol-11.0.3-orig/manifest/applet2.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet2.txt	2007-05-16 01:56:19.000000000 -0500
-@@ -0,0 +1,3 @@
-+Name: javax/vecmath/
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt
---- jmol-11.0.3-orig/manifest/applet3.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet3.txt	2007-05-16 01:56:47.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/g3d/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt
---- jmol-11.0.3-orig/manifest/applet4.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet4.txt	2007-05-16 01:57:05.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/adapter/smarter/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt
---- jmol-11.0.3-orig/manifest/applet5.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet5.txt	2007-05-16 01:57:23.000000000 -0500
-@@ -0,0 +1,4 @@
-+Name: org/openscience/jmol/ui/
-+Sealed: true
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt
---- jmol-11.0.3-orig/manifest/applet6.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet6.txt	2007-05-16 01:57:46.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/viewer/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt
---- jmol-11.0.3-orig/manifest/appletMain.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/appletMain.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,5 @@
-+Manifest-Version: 1.0
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt
---- jmol-11.0.3-orig/manifest/appletMonolithic.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/appletMonolithic.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,7 @@
-+Main-Class: JmolApplet
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt
---- jmol-11.0.3-orig/manifest/applet.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,2 @@
-+Manifest-Version: 1.0
-+Sealed: true
-\ No newline at end of file
-diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt
---- jmol-11.0.3-orig/manifest/application.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/application.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1 @@
-+Main-Class: org.openscience.jmol.app.Jmol
-diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt
---- jmol-11.0.3-orig/manifest/jvxl.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/jvxl.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1 @@
-+Main-Class: org.openscience.jvxl.Jvxl

diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
deleted file mode 100644
index c1b22e8..0000000
--- a/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
+++ /dev/null
@@ -1,313 +0,0 @@
---- build.xml	2011-02-25 12:59:43.000000000 -0600
-+++ build.xml.new	2011-02-27 12:16:02.398959959 -0600
-@@ -110,10 +110,6 @@
-           <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>
- 
-@@ -123,14 +119,6 @@
-           <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>
-     
-@@ -140,14 +128,6 @@
-           <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>
- 
-@@ -157,14 +137,6 @@
-           <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>
- 
-@@ -385,17 +357,12 @@
-   </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="${classes.dir}/org/openscience/jmol/Data" >
-       <fileset dir="build/doc/JmolHistory">
-         <include name="**/*.html" />
-@@ -587,18 +554,6 @@
-       <fileset dir="${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="${applet.classes.dir}">
-         <include name="org/jmol/minimize/**" />
-@@ -712,7 +667,6 @@
-         <include name="org/jmol/bspt/**" />
-         <include name="org/jmol/g3d/**" />
-         <include name="org/jmol/geodesic/**" />
--        <include name="org/jmol/i18n/**" />
-         <include name="org/jmol/modelset/**" />
-         <include name="org/jmol/script/**" />
-         <include name="org/jmol/shape/**" />
-@@ -738,7 +692,6 @@
-         <pathelement path="${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="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
-       </indexjars>
-     </jar>
-     <!-- changes to this must be replicated below for the signed applet -->
-@@ -851,16 +804,6 @@
-              keystore="selfSignedCertificate/selfSignedCertificate.store"
-              storepass="selfSignedCertificate" alias="selfSignedCertificate" />
- 
--    <for list="${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
-@@ -906,7 +849,6 @@
-         <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="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
-@@ -944,18 +886,6 @@
- 	      </fileset>
- 	    </jar>
- 
--	    <for list="${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/**" />
-@@ -1069,7 +999,6 @@
- 	        <include name="org/jmol/bspt/**" />
- 	        <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/**" />
-@@ -1095,7 +1024,6 @@
- 	        <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 -->
-@@ -1104,7 +1032,7 @@
- 	  </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}"/>
-@@ -1163,7 +1091,6 @@
-       <fileset dir=".">
-         <include name="applet.classes" />
-         <include name="build.xml" />
--        <include name="build-i18n.xml" />
-       </fileset>
-     </copy>
- 
-@@ -1246,7 +1173,6 @@
-       <fileset dir=".">
-         <include name="apisio.classes" />
-         <include name="build.xml" />
--        <include name="build-i18n.xml" />
-       </fileset>
-     </copy>
- 
-@@ -1342,7 +1268,7 @@
-   <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="${javadoc.dir}"/>
-     <delete dir="packaging/rpm/dist"/>
-@@ -1406,16 +1332,6 @@
-       <arg value="../../../doc/source/JmolGuide.docbook.xml" />
-       <arg value="../../${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"
-@@ -1430,26 +1346,6 @@
-       <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"
-@@ -1463,24 +1359,6 @@
-       <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="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
-   </target>
- 
-   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
-@@ -1494,24 +1372,6 @@
-       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
-       <arg value="../${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">
-@@ -1543,12 +1403,4 @@
-     <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/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz
deleted file mode 100644
index f0325b0..0000000
--- a/sci-chemistry/jmol/files/caffeine.xyz
+++ /dev/null
@@ -1,26 +0,0 @@
-24
-Caffeine
-H      -3.3804130    -1.1272367     0.5733036
-N       0.9668296    -1.0737425    -0.8198227
-C       0.0567293     0.8527195     0.3923156
-N      -1.3751742    -1.0212243    -0.0570552
-C      -1.2615018     0.2590713     0.5234135
-C      -0.3068337    -1.6836331    -0.7169344
-C       1.1394235     0.1874122    -0.2700900
-N       0.5602627     2.0839095     0.8251589
-O      -0.4926797    -2.8180554    -1.2094732
-C      -2.6328073    -1.7303959    -0.0060953
-O      -2.2301338     0.7988624     1.0899730
-H       2.5496990     2.9734977     0.6229590
-C       2.0527432    -1.7360887    -1.4931279
-H      -2.4807715    -2.7269528     0.4882631
-H      -3.0089039    -1.9025254    -1.0498023
-H       2.9176101    -1.8481516    -0.7857866
-H       2.3787863    -1.1211917    -2.3743655
-H       1.7189877    -2.7489920    -1.8439205
-C      -0.1518450     3.0970046     1.5348347
-C       1.8934096     2.1181245     0.4193193
-N       2.2861252     0.9968439    -0.2440298
-H      -0.1687028     4.0436553     0.9301094
-H       0.3535322     3.2979060     2.5177747
-H      -1.2074498     2.7537592     1.7203047

diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html
deleted file mode 100644
index 35a5d49..0000000
--- a/sci-chemistry/jmol/files/index.html
+++ /dev/null
@@ -1,14 +0,0 @@
-<html>
-  <head>
-    <title>Jmol Test Page</title>
-      <div align="center"> <b>All the Sugar and Twice the Caffeine.</b> <br><br>
-      <script src="./Jmol.js"></script>
-  </head>
-  <body>
-    <script>
-      jmolInitialize("./"); // REQUIRED
-      jmolApplet(400, "load ./caffeine.xyz");
-    </script></div>
-  </body>
-</html>
-

diff --git a/sci-chemistry/jmol/files/selfSignedCertificate.store b/sci-chemistry/jmol/files/selfSignedCertificate.store
deleted file mode 100644
index a7b0ccb..0000000
Binary files a/sci-chemistry/jmol/files/selfSignedCertificate.store and /dev/null differ

diff --git a/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
deleted file mode 100644
index 722c99d..0000000
--- a/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
+++ /dev/null
@@ -1,122 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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"
-HOMEPAGE="http://jmol.sourceforge.net/"
-KEYWORDS="~amd64 ~x86"
-LICENSE="LGPL-2.1"
-
-IUSE="client-only vhosts"
-
-WEBAPP_MANUAL_SLOT="yes"
-SLOT="0"
-
-COMMON_DEP="dev-java/commons-cli:1
-	dev-java/itext:0
-	sci-libs/jmol-acme:0
-	sci-libs/vecmath-objectclub:0"
-
-RDEPEND=">=virtual/jre-1.4
-	${COMMON_DEP}"
-DEPEND=">=virtual/jdk-1.4
-	!client-only? ( ${WEBAPP_DEPEND} )
-	${COMMON_DEP}"
-
-pkg_setup() {
-
-	if ! use client-only ; then
-		webapp_pkg_setup || die "Failed to setup webapp"
-	fi
-
-	java-pkg-2_pkg_setup
-
-}
-
-src_unpack() {
-
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${PV}/${PN}-nointl.patch
-	epatch "${FILESDIR}"/${PV}/${PN}-manifest.patch
-
-	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
-	cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \
-		|| die "Failed to install Cert file."
-
-	rm -v "${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
-
-	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
-
-}

diff --git a/sci-chemistry/jmol/metadata.xml b/sci-chemistry/jmol/metadata.xml
deleted file mode 100644
index ee65d2c..0000000
--- a/sci-chemistry/jmol/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-<email>je_fro@gentoo.org</email>
-<name>Jeff Gardner</name>
-</maintainer>
-<use>
-  <flag name='client-only'>Install the viewer only, no applet files for httpd
-    </flag>
-</use>
-</pkgmetadata>