diff options
-rw-r--r-- | sci-chemistry/jmol/Manifest | 6 | ||||
-rw-r--r-- | sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch | 96 | ||||
-rw-r--r-- | sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch (renamed from sci-chemistry/jmol/files/jmol-11.4.6-nointl.patch) | 597 | ||||
-rw-r--r-- | sci-chemistry/jmol/files/selfSignedCertificate.store | bin | 1516 -> 0 bytes | |||
-rw-r--r-- | sci-chemistry/jmol/jmol-12.2.27.ebuild (renamed from sci-chemistry/jmol/jmol-11.4.6.ebuild) | 34 |
5 files changed, 352 insertions, 381 deletions
diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest index 4ad5c1a..58e36de 100644 --- a/sci-chemistry/jmol/Manifest +++ b/sci-chemistry/jmol/Manifest @@ -2,6 +2,8 @@ AUX caffeine.xyz 1116 RMD160 92b432c6584cd927fa1bfb155ea41011ab7a82d8 SHA1 d0f35 AUX index.html 328 RMD160 60d2a573c228e018a864fd7d9cfc7554264ccd6b SHA1 7ab256d768d3a4da43b5e497dfb1c3a53a8068a9 SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451 AUX jmol-11.0.3-manifest.patch 3726 RMD160 03e1e11fdd29fb63de15934fff166348577084b0 SHA1 925a957bc30e1fbab9fd773dc07f83411f667d30 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd AUX jmol-11.4.6-nointl.patch 10695 RMD160 3d10af3e3c8debeb6680ab37e3e7fbf0cb871d4d SHA1 39f48d30de57e92f6399178a0605059eefda6373 SHA256 d34440c05b251e9392d9e4c85eceaeab9aaddac35be04e71781d95541252dc6f +AUX jmol-12.2.27-nointl.patch 13821 RMD160 4d6a6a598f4b550b6c2e3665c01b4f915d39c563 SHA1 2bc04f7a5e781f8628622a69f12d1f4a33b26140 SHA256 330a911405f00552d37a9c241c4a18b9d3e6812ce858933dbc4574df8248e345 AUX selfSignedCertificate.store 1516 RMD160 583b7bab5578e1e32f649388b7009dc654df1199 SHA1 88d9123bdc1a376ba00e00c8abef4751adefe3a5 SHA256 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5 -DIST jmol-11.4.6-full.tar.gz 16022367 RMD160 281fc0886df82763545fde94c040f3011ad0e672 SHA1 b83df223bc6c1ecb64c9d3de0e6baca2882f07fa SHA256 c5c4dd6d28adf15c25f4a5f795578d3f25f245b40b3a2bb5dc09b3e2f30b048b -EBUILD jmol-11.4.6.ebuild 3191 RMD160 f7a2d94379fa69d38053ee0ee0edc70398e83012 SHA1 93a0d72fe9f0e26edc0e6ea36fd6c1abd297b51a SHA256 767d3036f6e3ca0d1d37c3a08a2bee09f8fd938557dbecb438c15d9e4ebebd16 +DIST Jmol-12.2.27-full.tar.gz 29493780 RMD160 e0f530e92ed079b1debf9fbd5c720ad19ba71977 SHA1 663a3a83a1fff373cea624d4cec4fdd71efcd505 SHA256 f2ca3b810ea16a488f6f57003d2a407c8ac040d610479a7ae6d95631157db801 +DIST jmol-selfSignedCertificate.store.tar 10240 RMD160 a6d4df5f108a2c13074190569b95d3310439ea57 SHA1 218fff84df0c542b634ba08ed2e82d3d3280a481 SHA256 416744934991ef4f1fa298c0afc8e855d43771de2f2278ed3fbc60f707ea46b2 +EBUILD jmol-12.2.27.ebuild 3120 RMD160 6789d7bb9340d2674c4d101f7465baf22344bbbf SHA1 59d700dffcef83f8c96b98d2bc7a79ee7927d6a7 SHA256 8d998f8cc358528019b33b1a705bab31c23e0c79e37bd73e0b1cfd76dd776ea4 diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch deleted file mode 100644 index 3b43c21..0000000 --- a/sci-chemistry/jmol/files/jmol-11.0.3-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/jmol-11.4.6-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch index 252e236..0a43faa 100644 --- a/sci-chemistry/jmol/files/jmol-11.4.6-nointl.patch +++ b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch @@ -1,267 +1,330 @@ ---- jmol-11.4.6/build.xml.orig 2008-09-16 15:27:28.388008850 -0500 -+++ jmol-11.4.6/build.xml 2008-09-16 15:38:57.637384713 -0500 -@@ -104,10 +104,6 @@ - <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> - -@@ -117,14 +113,6 @@ - <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> - -@@ -134,14 +122,6 @@ - <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> - -@@ -151,14 +131,6 @@ - <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> - -@@ -350,17 +322,12 @@ - </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="${classes.dir}/org/openscience/jmol/Data" > - <fileset dir="build/doc/JmolHistory"> - <include name="**/*.html" /> -@@ -506,7 +473,6 @@ - <!-- note that this class is included in JmolApplet0.jar --> - <exclude name="org/jmol/api/JmolAppletInterface.class" /> - <include name="org/jmol/applet/**" /> -- <include name="org/jmol/i18n/**" /> - </fileset> - </jar> - -@@ -602,12 +568,6 @@ - </fileset> - </jar> - -- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" manifest="manifest/applet_i18n.txt" > -- <fileset dir="${applet.classes.dir}"> -- <include name="org/jmol/translation/**" /> -- </fileset> -- </jar> -- - - <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv --> - <!-- changes to this must be replicated below for the signed applet --> -@@ -636,7 +596,6 @@ - <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSpecial.jar" /> - <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" /> - <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Viewer.jar" /> -- <pathelement path="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" /> - </indexjars> - </jar> - <!-- changes to this must be replicated below for the signed applet --> -@@ -728,11 +687,6 @@ - - - -- <signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" -- signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar" -- keystore="selfSignedCertificate/selfSignedCertificate.store" -- storepass="selfSignedCertificate" alias="selfSignedCertificate" /> -- - <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv --> - <!-- this one must be treated specially because of jar indexing - we cannot simply rename the jar file, because the index has -@@ -762,7 +716,6 @@ - <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSpecial.jar" /> - <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" /> - <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Viewer.jar" /> -- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar" /> - </indexjars> - </jar> - <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar" -@@ -772,7 +725,7 @@ - </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}"/> -@@ -829,7 +782,6 @@ - <fileset dir="."> - <include name="applet.classes" /> - <include name="build.xml" /> -- <include name="build-i18n.xml" /> - </fileset> - </copy> - -@@ -908,7 +860,6 @@ - <fileset dir="."> - <include name="apisio.classes" /> - <include name="build.xml" /> -- <include name="build-i18n.xml" /> - </fileset> - </copy> - -@@ -1000,7 +951,7 @@ - <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="${javadoc.dir}"/> - <delete dir="packaging/rpm/dist"/> -@@ -1063,16 +1014,6 @@ - <arg value="../../../doc/source/JmolGuide.docbook.xml" /> - <arg value="../../${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" -@@ -1087,26 +1028,6 @@ - <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" -@@ -1120,24 +1041,6 @@ - <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="../${docbook-xsl}/html/docbook.xsl" /> -- </java> - </target> - - <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc" -@@ -1151,24 +1054,6 @@ - <arg value="../../doc/source/JmolAppletGuide.docbook.xml" /> - <arg value="../${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"> -@@ -1200,12 +1085,4 @@ - <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" /> - </target> - -- <!-- i18n stuff --> -- <target name="main-i18n" depends="classes"> -- <ant antfile="build-i18n.xml" target="main-i18n"/> -- </target> -- <target name="spotless-i18n"> -- <ant antfile="build-i18n.xml" target="spotless-i18n"/> -- </target> -- - </project> +--- 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/files/selfSignedCertificate.store b/sci-chemistry/jmol/files/selfSignedCertificate.store Binary files differdeleted file mode 100644 index a7b0ccb..0000000 --- a/sci-chemistry/jmol/files/selfSignedCertificate.store +++ /dev/null diff --git a/sci-chemistry/jmol/jmol-11.4.6.ebuild b/sci-chemistry/jmol/jmol-12.2.27.ebuild index 4d988b2..c8a4095 100644 --- a/sci-chemistry/jmol/jmol-11.4.6.ebuild +++ b/sci-chemistry/jmol/jmol-12.2.27.ebuild @@ -1,13 +1,19 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2012 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/${PN}/${P}-full.tar.gz" +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" @@ -20,33 +26,27 @@ SLOT="0" COMMON_DEP="dev-java/commons-cli dev-java/itext sci-libs/jmol-acme - sci-libs/vecmath-objectclub" - -RDEPEND=">=virtual/jre-1.4 + sci-libs/vecmath-objectclub + sci-libs/naga" +RDEPEND=">=virtual/jre-1.5 ${COMMON_DEP}" -DEPEND=">=virtual/jdk-1.4 +DEPEND=">=virtual/jdk-1.5 + dev-java/saxon:6.5 !client-only? ( ${WEBAPP_DEPEND} ) ${COMMON_DEP}" pkg_setup() { - if ! use client-only ; then - webapp_pkg_setup || die "Failed to setup webapp" - fi - + use client-only || webapp_pkg_setup java-pkg-2_pkg_setup - } src_unpack() { unpack ${A} - epatch "${FILESDIR}"/${P}-nointl.patch -# epatch "${FILESDIR}"/${P}-manifest.patch + cd "${S}" - mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory." - cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \ - || die "Failed to install Cert file." + epatch "${FILESDIR}"/${P}-nointl.patch rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die cd "${S}/jars" @@ -62,6 +62,8 @@ src_unpack() { 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 } |