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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 ([email protected]) +- * 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 ([email protected]) +- * 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
