[med-svn] r6931 - in trunk/packages: . cinema cinema/trunk cinema/trunk/debian cinema/trunk/debian/patches cinema/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Tue Jun 7 18:14:13 UTC 2011
Author: moeller
Date: 2011-06-07 18:14:13 +0000 (Tue, 07 Jun 2011)
New Revision: 6931
Added:
trunk/packages/cinema/
trunk/packages/cinema/trunk/
trunk/packages/cinema/trunk/debian/
trunk/packages/cinema/trunk/debian/README.Debian
trunk/packages/cinema/trunk/debian/README.source
trunk/packages/cinema/trunk/debian/changelog
trunk/packages/cinema/trunk/debian/compat
trunk/packages/cinema/trunk/debian/control
trunk/packages/cinema/trunk/debian/copyright
trunk/packages/cinema/trunk/debian/docs
trunk/packages/cinema/trunk/debian/menu.ex
trunk/packages/cinema/trunk/debian/patches/
trunk/packages/cinema/trunk/debian/patches/ant.patch
trunk/packages/cinema/trunk/debian/patches/application.patch
trunk/packages/cinema/trunk/debian/patches/series
trunk/packages/cinema/trunk/debian/rules
trunk/packages/cinema/trunk/debian/source/
trunk/packages/cinema/trunk/debian/source/format
trunk/packages/cinema/trunk/debian/watch
Log:
Dependency for mauve. Builds. Does not install, yet.
Added: trunk/packages/cinema/trunk/debian/README.Debian
===================================================================
--- trunk/packages/cinema/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/cinema/trunk/debian/README.Debian 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,6 @@
+cinema for Debian
+-----------------
+
+Cinema is a dependency for mauve. This shall just work.
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 07 Jun 2011 18:40:09 +0200
Added: trunk/packages/cinema/trunk/debian/README.source
===================================================================
--- trunk/packages/cinema/trunk/debian/README.source (rev 0)
+++ trunk/packages/cinema/trunk/debian/README.source 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,9 @@
+cinema for Debian
+-----------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+
Added: trunk/packages/cinema/trunk/debian/changelog
===================================================================
--- trunk/packages/cinema/trunk/debian/changelog (rev 0)
+++ trunk/packages/cinema/trunk/debian/changelog 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,5 @@
+cinema (3.0.23-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 07 Jun 2011 18:40:09 +0200
Added: trunk/packages/cinema/trunk/debian/compat
===================================================================
--- trunk/packages/cinema/trunk/debian/compat (rev 0)
+++ trunk/packages/cinema/trunk/debian/compat 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1 @@
+7
Added: trunk/packages/cinema/trunk/debian/control
===================================================================
--- trunk/packages/cinema/trunk/debian/control (rev 0)
+++ trunk/packages/cinema/trunk/debian/control 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,15 @@
+Source: cinema
+Section: unknown
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.9.1
+Homepage: <insert the upstream URL, if relevant>
+#Vcs-Git: git://git.debian.org/collab-maint/cinema.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/cinema.git;a=summary
+
+Package: cinema
+Architecture: all
+Depends: ${misc:Depends}
+Description: <insert up to 60 chars description>
+ <insert long description, indented with spaces>
Added: trunk/packages/cinema/trunk/debian/copyright
===================================================================
--- trunk/packages/cinema/trunk/debian/copyright (rev 0)
+++ trunk/packages/cinema/trunk/debian/copyright 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,36 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: cinema
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: <special license>
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+# If you want to use GPL v2 or later for the /debian/* files use
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
Added: trunk/packages/cinema/trunk/debian/docs
===================================================================
--- trunk/packages/cinema/trunk/debian/docs (rev 0)
+++ trunk/packages/cinema/trunk/debian/docs 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1 @@
+README
Added: trunk/packages/cinema/trunk/debian/menu.ex
===================================================================
--- trunk/packages/cinema/trunk/debian/menu.ex (rev 0)
+++ trunk/packages/cinema/trunk/debian/menu.ex 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,2 @@
+?package(cinema):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
+ title="cinema" command="/usr/bin/cinema"
Added: trunk/packages/cinema/trunk/debian/patches/ant.patch
===================================================================
--- trunk/packages/cinema/trunk/debian/patches/ant.patch (rev 0)
+++ trunk/packages/cinema/trunk/debian/patches/ant.patch 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,265 @@
+Index: cinema-3.0.23/src/uk/ac/man/bioinf/build.xml
+===================================================================
+--- cinema-3.0.23.orig/src/uk/ac/man/bioinf/build.xml 2011-06-07 19:37:22.000000000 +0200
++++ cinema-3.0.23/src/uk/ac/man/bioinf/build.xml 2011-06-07 19:37:56.000000000 +0200
+@@ -57,7 +57,7 @@
+ <property name="javadoc.packages" value="uk.ac.man.bioinf.*" />
+
+ <!-- Support for texi doclet. Set the first to use -->
+- <property name="javadoc.use.texidoc"/>
++ <property name="javadoc.use.texidoc" value="." />
+ <property name="javadoc.texidoc.path" value="."/>
+ <property name="javadoc.texi" value="${javadoc}" />
+
+@@ -91,6 +91,9 @@
+ <fileset dir="${ext}">
+ <include name="**/*.jar" />
+ </fileset>
++ <fileset dir="/usr/share/java">
++ <include name="**/*.jar" />
++ </fileset>
+
+ </path>
+
+@@ -108,6 +111,7 @@
+ <javac classpathref="project.class.path"
+ debug="${debug}"
+ srcdir="${src}"
++ source="1.4"
+ destdir="${classes}">
+ <include name="uk/**/*.java" />
+ <exclude name="${exclude}" />
+@@ -327,7 +331,3 @@
+ <target name="all" description="Build everything from scratch"
+ depends="clean,prepare,dist_build,javadoc" />
+ </project>
+-
+-
+-
+-
+\ No newline at end of file
+Index: cinema-3.0.23/home/moeller/alioth/debian-med/packages/cinema/cinema-3.0.23/src/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.java
+===================================================================
+--- cinema-3.0.23.orig/home/moeller/alioth/debian-med/packages/cinema/cinema-3.0.23/src/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.java 2011-06-07 19:38:20.000000000 +0200
++++ /dev/null 1970-01-01 00:00:00.000000000 +0000
+@@ -1,96 +0,0 @@
+-/*
+- * This program is free software; you can redistribute it and/or modify
+- * it under the terms of the GNU General Public License as published by
+- * the Free Software Foundation; either version 2 of the License, or
+- * (at your option) any later version.
+- *
+- * This program is distributed in the hope that it will be useful,
+- * but WITHOUT ANY WARRANTY; without even the implied warranty of
+- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+- * GNU General Public License for more details.
+- *
+- * You should have received a copy of the GNU General Public License
+- * along with this program; if not, write to the Free Software
+- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+-*/
+-
+-/*
+- * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+- * whilst at the University of Manchester as a Pfizer post-doctoral
+- * Research Fellow.
+- *
+- * The initial code base is copyright by Pfizer, or the University
+- * of Manchester. Modifications to the initial code base are copyright
+- * of their respective authors, or their employers as appropriate.
+- * Authorship of the modifications may be determined from the ChangeLog
+- * placed at the end of this file
+- */
+-
+-package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+-import org.xml.sax.InputSource;
+-import org.xml.sax.SAXException;
+-import org.xml.sax.XMLReader;
+-import org.xml.sax.helpers.DefaultHandler;
+-import org.xml.sax.helpers.XMLReaderFactory;
+-import uk.ac.man.bioinf.apps.cinema.resources.CinemaResources;
+-import uk.ac.man.bioinf.apps.xml.XMLParserFactory;
+-import uk.ac.man.bioinf.debug.Debug;
+-
+-
+-/**
+- * CinemaXMLParserFactory.java
+- *
+- *
+- * Created: Mon Sep 18 18:59:17 2000
+- *
+- * @author Phillip Lord
+- * @version $Id: CinemaXMLParserFactory.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+- */
+-
+-public class CinemaXMLParserFactory implements XMLParserFactory
+-{
+-
+- public XMLReader getXMLParser()
+- {
+- try{
+-
+- XMLReader read = XMLReaderFactory.createXMLReader( "org.apache.xerces.parsers.SAXParser" );
+- read.setEntityResolver
+- ( new DefaultHandler(){
+- public InputSource resolveEntity( String publicId, String systemId ) throws SAXException
+- {
+- if( systemId.equals( "file:module.dtd" ) ){
+- return new InputSource( CinemaResources.getModuleDTDAsResource() );
+- }
+-
+- return super.resolveEntity( publicId, systemId );
+- }
+- });
+- return read;
+- }
+- catch( Exception exp ){
+- if( Debug.debug )
+- Debug.throwable( this, exp );
+- }
+- return null;
+- }
+-} // CinemaXMLParserFactory
+-
+-
+-
+-/*
+- * ChangeLog
+- * $Log: CinemaXMLParserFactory.java,v $
+- * Revision 1.3 2001/04/11 17:04:41 lord
+- * Added License agreements to all code
+- *
+- * Revision 1.2 2000/12/18 12:09:23 jns
+- * o getting rid of system.out.println to avoid noisy output out of debug
+- * mode
+- *
+- * Revision 1.1 2000/09/25 16:35:34 lord
+- * Changes made so that the XMLParser used is no longer hard coded
+- * but comes from a factory. This allows for instance giving the parser a
+- * custom entity resolver.
+- *
+- */
+Index: cinema-3.0.23/home/moeller/alioth/debian-med/packages/cinema/cinema-3.0.23/src/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.java
+===================================================================
+--- cinema-3.0.23.orig/home/moeller/alioth/debian-med/packages/cinema/cinema-3.0.23/src/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.java 2011-06-07 19:38:40.000000000 +0200
++++ /dev/null 1970-01-01 00:00:00.000000000 +0000
+@@ -1,119 +0,0 @@
+-/*
+- *This library is free software; you can redistribute it and/or
+- *modify it under the terms of the GNU Lesser General Public
+- *License as published by the Free Software Foundation; either
+- *version 2.1 of the License, or (at your option) any later version.
+- *
+- *This library is distributed in the hope that it will be useful,
+- *but WITHOUT ANY WARRANTY; without even the implied warranty of
+- *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+- *Lesser General Public License for more details.
+- *
+- *You should have received a copy of the GNU Lesser General Public
+- *License along with this library; if not, write to the Free Software
+- *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+-*/
+-
+-/*
+- * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+- * whilst at the University of Manchester as a Pfizer post-doctoral
+- * Research Fellow.
+- *
+- * The initial code base is copyright by Pfizer, or the University
+- * of Manchester. Modifications to the initial code base are copyright
+- * of their respective authors, or their employers as appropriate.
+- * Authorship of the modifications may be determined from the ChangeLog
+- * placed at the end of this file
+- */
+-
+-package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
+-import org.xml.sax.InputSource;
+-import org.xml.sax.SAXException;
+-import org.xml.sax.XMLReader;
+-import org.xml.sax.helpers.DefaultHandler;
+-import org.xml.sax.helpers.XMLReaderFactory;
+-import uk.ac.man.bioinf.debug.Debug;
+-
+-
+-/**
+- * DefaultXMLParser.java
+- *
+- *
+- * Created: Mon May 8 21:08:32 2000
+- *
+- * @author Phillip Lord
+- * @version $Id: DefaultXMLParser.java,v 1.5 2001/04/11 17:04:42 lord Exp $
+- */
+-
+-public class DefaultXMLParser implements XMLParserFactory
+-{
+- public XMLReader getXMLParser()
+- {
+- try{
+- XMLReader read = XMLReaderFactory.createXMLReader( "org.apache.xerces.parsers.SAXParser" );
+- read.setEntityResolver
+- ( new DefaultHandler(){
+- public InputSource resolveEntity( String publicId, String systemId ) throws SAXException
+- {
+- InputSource retn = super.resolveEntity( publicId, systemId );
+- System.out.println( "ENTITY:- " + retn + " pub " + publicId + " sys " + systemId );
+- return retn;
+- }
+- });
+- return read;
+- }
+- catch( Exception exp ){
+- if( Debug.debug )
+- Debug.throwable( this, exp );
+- }
+- return null;
+- }
+-} // DefaultXMLParser
+-
+-
+-
+-/*
+- * ChangeLog
+- * $Log: DefaultXMLParser.java,v $
+- * Revision 1.5 2001/04/11 17:04:42 lord
+- * Added License agreements to all code
+- *
+- * Revision 1.4 2000/12/18 12:12:53 jns
+- * o getting rid of system.out.println to avoid noisy output out of debug
+- * mode
+- *
+- * Revision 1.3 2000/10/19 17:51:15 lord
+- * Import rationalisation
+- *
+- * Revision 1.2 2000/09/25 16:35:34 lord
+- * Changes made so that the XMLParser used is no longer hard coded
+- * but comes from a factory. This allows for instance giving the parser a
+- * custom entity resolver.
+- *
+- * Revision 1.1 2000/05/15 16:23:53 lord
+- * Initial checkin
+- *
+- */
+-
+-/*
+- * ChangeLog
+- * $Log: DefaultXMLParser.java,v $
+- * Revision 1.5 2001/04/11 17:04:42 lord
+- * Added License agreements to all code
+- *
+- * Revision 1.4 2000/12/18 12:12:53 jns
+- * o getting rid of system.out.println to avoid noisy output out of debug
+- * mode
+- *
+- * Revision 1.3 2000/10/19 17:51:15 lord
+- * Import rationalisation
+- *
+- * Revision 1.2 2000/09/25 16:35:34 lord
+- * Changes made so that the XMLParser used is no longer hard coded
+- * but comes from a factory. This allows for instance giving the parser a
+- * custom entity resolver.
+- *
+- * Revision 1.1 2000/05/15 16:23:53 lord
+- * Initial checkin
+- *
+- */
Added: trunk/packages/cinema/trunk/debian/patches/application.patch
===================================================================
--- trunk/packages/cinema/trunk/debian/patches/application.patch (rev 0)
+++ trunk/packages/cinema/trunk/debian/patches/application.patch 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,52 @@
+Index: cinema-3.0.23/bin/cinema
+===================================================================
+--- cinema-3.0.23.orig/bin/cinema 2011-06-07 19:41:52.000000000 +0200
++++ cinema-3.0.23/bin/cinema 2011-06-07 20:12:19.000000000 +0200
+@@ -16,6 +16,7 @@
+ ## to this is probably to do as much of the command liner parsing in
+ ## Java as possible.
+
++set -e
+
+ ## This is the location of the main install directory where Cinema
+ ## should find all most of its jar files.
+@@ -66,8 +67,15 @@
+ ext_jars=${ext_jars}:$jar_file
+ done
+
++#for jar_file in $( find /usr/share/java/ -name "*.jar" -a ! -type l )
++for jar_file in /usr/share/java/gnu-getopt.jar /usr/share/java/regexp.jar /usr/share/java/xalan2.jar /usr/share/java/nekohtml.jar /usr/share/java/nekohtmlXni.jar
++do
++ [ -r $jar_file ] || echo "Not found: $jar_file"
++ system_jars=${system_jars}:$jar_file
++done
++
+ # classpath
+-classpath=${user_jars}${cinema_jars}${ext_jars}
++classpath=${user_jars}${cinema_jars}${ext_jars}:${system_jars}
+
+
+ ##
+@@ -81,4 +89,5 @@
+ echo "Running Cinema as ${COMMAND_LINE}"
+ fi
+
++echo "executing java -classpath ${classpath} uk.ac.man.bioinf.apps.cinema.Cinema $OTHER_ARGUMENTS $*"
+ java -classpath ${classpath} uk.ac.man.bioinf.apps.cinema.Cinema $OTHER_ARGUMENTS $*
+Index: cinema-3.0.23/bin/cinema.pl
+===================================================================
+--- cinema-3.0.23.orig/bin/cinema.pl 2011-06-07 19:43:56.000000000 +0200
++++ cinema-3.0.23/bin/cinema.pl 2011-06-07 19:44:32.000000000 +0200
+@@ -63,7 +63,11 @@
+ $ext_jars.=":$jarfile";
+ }
+
+-my $classpath="$user_jars$cinema_jars$ext_jars";
++foreach $jarfile ( glob( "/usr/share/java/*jar" ) ){
++ $system_jars.=":$jarfile";
++}
++
++my $classpath="$user_jars$cinema_jars$ext_jars$system_jars";
+
+ if( $VERBOSE ){
+ print "java -classpath $classpath $JVM_OPTIONS uk.ac.man.bioinf.apps.cinema.Cinema @ARGV";
Added: trunk/packages/cinema/trunk/debian/patches/series
===================================================================
--- trunk/packages/cinema/trunk/debian/patches/series (rev 0)
+++ trunk/packages/cinema/trunk/debian/patches/series 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,3 @@
+ant.patch
+application.patch
+ioexception.patch
Added: trunk/packages/cinema/trunk/debian/rules
===================================================================
--- trunk/packages/cinema/trunk/debian/rules (rev 0)
+++ trunk/packages/cinema/trunk/debian/rules 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+dh_override_auto_build:
+ mkdir -p classes/ext
+ cd src/uk/ac/man/bioinf && ant dist_build
+
+
+get-orig-source:
+ # this version is mostly historical
+ [ -r cinema-3_0_23.tar.gz ] || wget http://homepages.cs.ncl.ac.uk/phillip.lord/download/java/cinema/cinema-3_0_23.tar.gz
+ tar xzvf cinema-3_0_23.tar.gz
+ cd cinema-3_0_23 && rm -r classes lib
+ mv cinema-3_0_23 cinema-3.0.23
+ tar czvf cinema-3.0.23.orig.tar.gz cinema-3.0.23
+ rm -r cinema-3.0.23
+ rm cinema-3_0_23.tar.gz
Property changes on: trunk/packages/cinema/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/cinema/trunk/debian/source/format
===================================================================
--- trunk/packages/cinema/trunk/debian/source/format (rev 0)
+++ trunk/packages/cinema/trunk/debian/source/format 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/cinema/trunk/debian/watch
===================================================================
--- trunk/packages/cinema/trunk/debian/watch (rev 0)
+++ trunk/packages/cinema/trunk/debian/watch 2011-06-07 18:14:13 UTC (rev 6931)
@@ -0,0 +1,8 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+http://homepages.cs.ncl.ac.uk/phillip.lord/download/java/cinema/cinema-([0-9_]+).tar.gz
More information about the debian-med-commit
mailing list