[med-svn] r18647 - in trunk/packages/biojava4-live/trunk: . debian debian/patches debian/source
Olivier Sallou
osallou at moszumanska.debian.org
Fri Jan 30 21:17:40 UTC 2015
Author: osallou
Date: 2015-01-30 21:17:39 +0000 (Fri, 30 Jan 2015)
New Revision: 18647
Added:
trunk/packages/biojava4-live/trunk/debian/
trunk/packages/biojava4-live/trunk/debian/README.Debian
trunk/packages/biojava4-live/trunk/debian/README.source
trunk/packages/biojava4-live/trunk/debian/biojava-doc.docs
trunk/packages/biojava4-live/trunk/debian/biojava-doc.install
trunk/packages/biojava4-live/trunk/debian/build.xml
trunk/packages/biojava4-live/trunk/debian/changelog
trunk/packages/biojava4-live/trunk/debian/compat
trunk/packages/biojava4-live/trunk/debian/control
trunk/packages/biojava4-live/trunk/debian/copyright
trunk/packages/biojava4-live/trunk/debian/docs
trunk/packages/biojava4-live/trunk/debian/get-orig-source
trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.doc-base
trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.install
trunk/packages/biojava4-live/trunk/debian/libbiojava3.0-java.jlibs
trunk/packages/biojava4-live/trunk/debian/patches/
trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping
trunk/packages/biojava4-live/trunk/debian/patches/fix_code_to_support_latest_jmol
trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates
trunk/packages/biojava4-live/trunk/debian/patches/fix_uselog4j1
trunk/packages/biojava4-live/trunk/debian/patches/java8_compatibility.patch
trunk/packages/biojava4-live/trunk/debian/patches/series
trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json
trunk/packages/biojava4-live/trunk/debian/rules
trunk/packages/biojava4-live/trunk/debian/source/
trunk/packages/biojava4-live/trunk/debian/source/format
trunk/packages/biojava4-live/trunk/debian/watch
Log:
[svn-inject] Application des modifications Debian (4.0.0+dfsg-1) pour le tronc
Property changes on: trunk/packages/biojava4-live/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/biojava4-live/trunk/debian/README.Debian
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/README.Debian 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,23 @@
+biojava for Debian
+------------------
+
+This package provide biojava libraries, made up of multiple libraries, dependent on biojava-core and other libraries.
+To make use of thos libraries, the following libraries are needed in the classpath:
+ <fileset dir="/usr/share/java">
+ <include name="commons-cli.jar"/>
+ <include name="commons-collections.jar"/>
+ <include name="commons-dbcp.jar"/>
+ <include name="commons-pool.jar"/>
+ <include name="junit.jar"/>
+ <include name="guava.jar"/>
+ <include name="jgrapht0.8.jar"/>
+ <include name="Jmol.jar"/>
+ <include name="json-lib.jar"/>
+ <include name="biojava3-core.jar"/>
+ <include name="biojava3-forester.jar"/>
+ </fileset>
+ <fileset dir="/usr/share/icedtea-web">
+ <include name="netx.jar"/>
+ </fileset>
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Added: trunk/packages/biojava4-live/trunk/debian/README.source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/README.source (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/README.source 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,14 @@
+biojava for Debian
+------------------
+
+Biojava3 uses the forester library version 0.955.
+The source version is hosted in Biojava repo only and does not
+match any release available in forester web site. To manage,
+a specific biojava3-forester library is created.
+
+The get-orig-source embeds this library version in the code.
+
+json.org dependency is replaced by json-simple with a patch for biojava3-ws.
+Future release will use json-lib
+
+Some tests are skipped due to errors dependending on context (nfs dirs), remote access required....
Added: trunk/packages/biojava4-live/trunk/debian/biojava-doc.docs
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/biojava-doc.docs (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/biojava-doc.docs 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1 @@
+#DOCS#
Added: trunk/packages/biojava4-live/trunk/debian/biojava-doc.install
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/biojava-doc.install (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/biojava-doc.install 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1 @@
+#DOCS#
Added: trunk/packages/biojava4-live/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/build.xml (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/build.xml 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,120 @@
+<?xml version="1.0" ?>
+<project name="BJLIB" default="jar" basedir=".">
+ <!-- Directory structure -->
+ <property name="build.dir" location="../build/BJLIB"/>
+ <property name="test.dir" location="../buildtest/BJLIB"/>
+ <property name="dist.dir" location="../dist"/>
+ <property name="src.dir" location="src/main/java"/>
+ <property name="resources.dir" location="src/main/resources"/>
+ <property name="test.src.dir" location="src/test/java"/>
+ <property name="test.resources.dir" location="src/test/resources"/>
+ <property name="lib.dir" location="/usr/share/java"/>
+ <property name="docs.dir" location="../javadoc"/>
+ <property name="docs.lib.dir" location="../doc/BJLIB"/>
+ <property name="class.dir" location="${build.dir}/classes"/>
+ <property name="test.class.dir" location="${test.dir}/classes"/>
+
+ <property name="project.name" value="biojava"/>
+ <property name="debug" value="true"/>
+ <property name="optimized" value="true"/>
+ <property name="project.version" value="1.8.2"/>
+ <property environment="env"/>
+ <property name="project.jarfile.name" value="BJLIB.jar"/>
+
+ <property name="class.path" value="${lib.dir}/commons-logging.jar ${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar"/>
+
+ <path id="compile.classpath">
+ <fileset dir="${lib.dir}">
+ <include name="commons-cli.jar"/>
+ <include name="commons-collections3.jar"/>
+ <include name="commons-dbcp.jar"/>
+ <include name="commons-logging.jar"/>
+ <include name="commons-pool.jar"/>
+ <include name="commons-codec.jar"/>
+ <include name="itext5.jar"/>
+ <include name="Jmol.jar"/>
+ <include name="junit4.jar"/>
+ <include name="guava.jar"/>
+ <include name="jgrapht0.8.jar"/>
+ <include name="JmolApplet.jar"/>
+ <include name="hamcrest.jar"/>
+ <include name="json-simple.jar"/>
+ <include name="log4j2.jar"/>
+ <include name="slf4j-api.jar"/>
+ <include name="log4j-over-slf4j.jar"/>
+ </fileset>
+ <fileset dir="${dist.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <fileset dir="/usr/share/icedtea-web">
+ <include name="netx.jar"/>
+ </fileset>
+ </path>
+
+
+ <target name="clean">
+ <echo level="info">Cleaning build directories</echo>
+ <delete verbose="true" includeEmptyDirs="true">
+ <fileset dir="${build.dir}" includes="**"/>
+ <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
+ </delete>
+ </target>
+
+ <target name="javadocs">
+ <mkdir dir="${docs.dir}"/>
+ <mkdir dir="${docs.lib.dir}"/>
+ <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*" encoding="UTF-8">
+ <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
+ </javadoc>
+ </target>
+
+ <target name="compile">
+ <mkdir dir="${class.dir}"/>
+ <mkdir dir="${dist.dir}"/>
+ <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
+ </javac>
+ <copy todir="${class.dir}" failonerror="false">
+ <fileset dir="${resources.dir}"/>
+ </copy>
+ </target>
+
+ <target name="compile-test">
+ <mkdir dir="${test.class.dir}"/>
+ <javac srcdir="${test.src.dir}" destdir="${test.class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true">
+ </javac>
+ <copy todir="${test.class.dir}" failonerror="false">
+ <fileset dir="${test.resources.dir}"/>
+ </copy>
+ <copy todir="${test.class.dir}" failonerror="false">
+ <fileset dir="${src.dir}"/>
+ </copy>
+ </target>
+
+ <path id="test.classpath">
+ <path refid="compile.classpath"/>
+ <pathelement location="${test.class.dir}" />
+ </path>
+
+ <target name="test" depends="compile-test">
+ <junit haltonfailure="yes" printsummary="yes" fork="true">
+ <classpath refid="test.classpath"/>
+ <formatter type="plain" usefile="false" />
+ <batchtest>
+ <fileset dir="${test.class.dir}" includes="**/*Test.class" excludes="**/Abstract*.class" />
+ </batchtest>
+ </junit>
+ </target>
+
+ <target name="jar" depends="compile">
+ <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
+ <manifest>
+ <attribute name="Built-By" value="Debian-Med team"/>
+ <attribute name="Class-Path" value="${class.path}"/>
+ <attribute name="Specification-Title" value="BioJava"/>
+ <attribute name="Specification-Version" value="${project.version}"/>
+ </manifest>
+ </jar>
+ </target>
+
+</project>
+
Added: trunk/packages/biojava4-live/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/changelog (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/changelog 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,7 @@
+biojava4-live (4.0.0+dfsg-1) UNRELEASED; urgency=medium
+
+ * BioJava4 packaging
+ [ needs Jmol upgrade, build of biojava-structure-gui meanwhile ]
+ [ failing test org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest ]
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 30 Jan 2015 17:24:21 +0100
Added: trunk/packages/biojava4-live/trunk/debian/compat
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/compat (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/compat 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1 @@
+8
Added: trunk/packages/biojava4-live/trunk/debian/control
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/control (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/control 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,82 @@
+Source: biojava4-live
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
+ libcommons-collections3-java, libcommons-pool-java (>= 1.1),
+ libcommons-logging-java,
+ libcommons-cli-java, libguava-java (>= 17.0),
+ libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java,
+ default-jdk (>= 1:1.6), junit4,javahelper (>=0.25),
+ ant-optional, icedtea-netx, libhamcrest-java,
+ libjson-simple-java (>=1.1.1),
+ liblog4j2-java, libslf4j-java
+Build-Depends: debhelper (>= 9), ant
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava4/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava4/trunk/
+Homepage: http://www.biojava.org
+
+Package: libbiojava4.0-java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libcommons-pool-java (>= 1.1),
+ libcommons-collections3-java,
+ libcommons-dbcp-java (>= 1.1),
+ libcommons-logging-java,
+ libhsqldb-java,
+ libbytecode-java,
+ icedtea-netx,
+ libjson-simple-java,
+ libcommons-codec-java,
+ libitext5-java (>= 5.4.1),
+ libjmol-java,
+ liblog4j2-java,
+ libguava-java (>= 17.0),
+ libslf4j-java
+Suggests: java-virtual-machine, libjgrapht-java, libbiojava4-java, libbiojava4-java-doc
+Description: Java API to biological data and applications (version 4)
+ This package presents the Open Source Java API to biological databases
+ and a series of mostly sequence-based algorithms.
+ .
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+
+Package: libbiojava4-java
+Architecture: all
+Depends: libbiojava4.0-java, ${misc:Depends}
+Provides: libbiojava4-java
+Description: Java API to biological data and applications (default version)
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+ .
+ BioJava is provided by a vibrant community which meets annually at
+ the Bioinformatics Open Source Conference (BOSC) that traditionally
+ accompanies the Intelligent Systems in Molecular Biology (ISMB)
+ meeting. Much like BioPerl, the employment of this library is valuable
+ for everybody active in the field because of the many tricks of the
+ trade one learns just by communicating on the mailing list.
+ .
+ This is a wrapper package which should enable smooth upgrades to new
+ versions.
+
+Package: libbiojava4-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: konqueror|html-browser
+Suggests: libbiojava4-java-demos, libbiojava4-java
+Description: [Biology] Documentation for BioJava
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data.
+ .
+ This package contains the HTML documentation describing the API of BioJava
+ which was generated automatically by JavaDoc.
+
Added: trunk/packages/biojava4-live/trunk/debian/copyright
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/copyright (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/copyright 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,73 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: biojava3
+Source: http://www.biojava.org/
+
+Files: biojava4-forester
+Copyright: 2008-2009 Christian M. Zmasek
+ 2008-2009 Burnham Institute for Medical Research
+License: LGPL-2.1+
+ This package 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 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 Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+
+Files: *
+Copyright: 2008-2012 the Individual authors who contributed the code,
+ as identified by the @authors tag of the respective source file.
+ BioJava Developers <biojava-l at biojava.org>
+ Scooter Willis <willishf at gmail dot com>, Mark Chapman, Andy Yates,
+ Richard Holland, Mark Reinhold, brandstaetter, Thomas Down, Unidata Program Center,
+ Ronald Tschalar, Andreas Prlic, Amr AL-Hossary, Jianjiong Gao, Spencer Bliven,
+ Jules Jacobsen <jacobsen at ebi.ac.uk>, J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
+ A.TULINSKY, ap3, The MathWorks Inc. and the National Institute of Standards and Technology,
+ Spencer Bliven <sbliven at ucsd.edu>, mulvaney, Peter Rose, Horvath Tamas, Peter Lackner,
+ Koh Chuan Hock, Expasy4J, Benjamin Schuster-Böckle, Peter Troshin
+License: LGPL-2.1+
+ This package 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 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 Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou 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".
+
Added: trunk/packages/biojava4-live/trunk/debian/docs
===================================================================
Added: trunk/packages/biojava4-live/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/get-orig-source 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download |
+ grep "Newest version on remote site is .* local version is .*" |
+ head -n 1 |
+ sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+
+
+mkdir -p ../tarballs
+
+cd ../tarballs
+UTAR="biojava-${VERSION}.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+mv biojava-biojava-${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
+
+cd $PKG-${VERSION}.orig
+ rm -rf target
+ rm -rf biojava/dist/*.jar
+
+mkdir -p biojava4-forester/src/main/java
+cd biojava4-forester/src/main/java
+ #wget http://www.biojava.org/download/maven/org/forester/forester-1.005-sources/1.005/forester-1.005-sources-1.005.jar
+ wget http://www.biojava.org/download/maven/org/forester/forester-lgpl/1.005/forester-lgpl-1.005-sources.jar
+ #jar xf forester-1.005-sources-1.005.jar
+ jar xf forester-lgpl-1.005-sources.jar
+ find . -name *.class | xargs rm -f
+ rm -f resources/*.jar
+ rm forester-lgpl-1.005-sources.jar
+ #rm forester-1.005-sources-1.005.jar
+cd ../../../..
+cd ..
+
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}+dfsg.orig.tar.bz2 ${PKG}-${VERSION}.orig
+rm -rf ${PKG}-${VERSION}.orig
+
+rm ${UTAR}
+
Property changes on: trunk/packages/biojava4-live/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.doc-base
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.doc-base (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.doc-base 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,26 @@
+Document: biojava3
+Title: biojava3 API
+Author: BioJava developers
+Abstract: Javadoc-generated API for the BioJava library.
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, DAS client and server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+ .
+ BioJava is provided by a vibrant community which meets annually at
+ the Bioinformatics Open Source Conference (BOSC) that traditionally
+ accompanies the Intelligent Systems in Molecular Biology (ISMB)
+ meeting. Much like BioPerl, the employment of this library is valuable
+ for everybody active in the field because of the many tricks of the
+ trade one learns just by communicating on the mailing list.
+ .
+ If using BioJava, please cite: R.C.G. Holland, T. Down, M. Pocock,
+ A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates,
+ M. Heuer; M.J. Schreiber (2008) "BioJava: an Open-Source Framework
+ for Bioinformatics" Bioinformatics 24(18):2096-2097.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/libbiojava3-java/api/index.html
+Files: /usr/share/doc/libbiojava3-java/api/*.html /usr/share/doc/libbiojava3-java/api/*/*/*/*.html /usr/share/doc/libbiojava3-java/api/*/*/*/*/*.html /usr/share/doc/libbiojava3-java/api/*/*/*/*/*/*.html /usr/share/doc/libbiojava3-java/api/*/*/*/*/*/*/*/*.html
Added: trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.install
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.install (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.install 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,3 @@
+doc/biojava/* usr/share/doc/libbiojava3-java/api
+
+
Added: trunk/packages/biojava4-live/trunk/debian/libbiojava3.0-java.jlibs
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/libbiojava3.0-java.jlibs (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/libbiojava3.0-java.jlibs 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,12 @@
+dist/biojava3-forester.jar
+dist/biojava3-core.jar
+dist/biojava3-phylo.jar
+dist/biojava3-alignment.jar
+dist/biojava3-aa-prop.jar
+dist/biojava3-genome.jar
+dist/biojava3-sequencing.jar
+dist/biojava3-structure.jar
+dist/biojava3-structure-gui.jar
+dist/biojava3-modfinder.jar
+dist/biojava3-protein-disorder.jar
+dist/biojava3-ws.jar
Added: trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,28 @@
+Subject: ASCII error in pbuilder
+Description: unmappable character for encoding ASCII
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2012-12-05
+Forwarded: yes
+Bug: http://code.google.com/p/forester/issues/detail?id=1
+--- a/biojava3-forester/src/main/java/org/forester/test/Test.java
++++ b/biojava3-forester/src/main/java/org/forester/test/Test.java
+@@ -1310,7 +1310,7 @@
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
+- .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
++ .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489-493." ) ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueRange.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueRange.java
+@@ -33,7 +33,7 @@
+
+ /**
+ * A chain, a start residue, and an end residue. May also store a length value. Because of insertion codes, this length
+- * is not necessarily {@code end − start}.
++ * is not necessarily {@code end - start}.
+ *
+ * @author dmyerstu
+ * @see ResidueNumber
Added: trunk/packages/biojava4-live/trunk/debian/patches/fix_code_to_support_latest_jmol
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_code_to_support_latest_jmol (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_code_to_support_latest_jmol 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,26 @@
+Subject: Latest JMOL library requires mode method definition
+Author: Olivier Sallou <osallou at irisa.fr>
+Description: Add required interface method from latest JMOL library definition
+Last--Updated: 2012-05-29
+
+--- a/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
++++ b/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
+@@ -42,7 +42,17 @@
+ public void setTextField (JTextField statusField) {
+ status = statusField;
+ }
+-
++
++ public void resizeInnerPanel(java.lang.String arg0) {
++ }
++
++ public boolean notifyEnabled(org.jmol.constant.EnumCallback callback) {
++ return false;
++ }
++
++ public void notifyCallback(EnumCallback type, Object[] data) {
++ }
++
+ public String createImage(String arg0, String arg1, Object arg2, int arg3) {
+ // TODO Auto-generated method stub
+ return null;
Added: trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,18 @@
+Subject: iText move a class to an other package
+Description: one of the class from iText moved to an other package.
+ Upstream code needs to refer to this new package and depends on
+ newer release if iText5
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-06-18
+Forwarded: no
+--- a/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
++++ b/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
+@@ -39,7 +39,7 @@
+ import com.itextpdf.text.DocumentException;
+ import com.itextpdf.text.FontFactory;
+ import com.itextpdf.text.Rectangle;
+-import com.itextpdf.text.pdf.DefaultFontMapper;
++import com.itextpdf.awt.DefaultFontMapper;
+ import com.itextpdf.text.pdf.PdfContentByte;
+ import com.itextpdf.text.pdf.PdfWriter;
+
Added: trunk/packages/biojava4-live/trunk/debian/patches/fix_uselog4j1
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_uselog4j1 (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_uselog4j1 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,74 @@
+Subject: use log4j v1.X
+Description: upstream use log4j v2.X which is not yet available in Debian.
+There is no specific v2 API usage, so applying a patch to use the log4j
+version available in Debian waiting for new version availability.
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2014-02-01
+Forwarded: no
+--- a/biojava3-structure/pom.xml
++++ b/biojava3-structure/pom.xml
+@@ -29,9 +29,9 @@
+ </dependency>
+
+ <dependency>
+- <groupId>org.apache.logging.log4j</groupId>
+- <artifactId>log4j-core</artifactId>
+- <version>2.0-beta7</version>
++ <groupId>log4j</groupId>
++ <artifactId>log4j</artifactId>
++ <version>1.2.17</version>
+ </dependency>
+
+ <!-- <dependency> <groupId>org.biojava</groupId> <artifactId>biojava3-core</artifactId>
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java
+@@ -23,8 +23,8 @@
+ import java.io.InputStream;
+ import java.net.URL;
+
+-import org.apache.logging.log4j.LogManager;
+-import org.apache.logging.log4j.Logger;
++import org.apache.log4j.LogManager;
++import org.apache.log4j.Logger;
+ import org.w3c.dom.Element;
+ import org.w3c.dom.NodeList;
+
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java
+@@ -25,8 +25,8 @@
+ import java.util.ArrayList;
+ import java.util.List;
+
+-import org.apache.logging.log4j.LogManager;
+-import org.apache.logging.log4j.Logger;
++import org.apache.log4j.LogManager;
++import org.apache.log4j.Logger;
+ import org.w3c.dom.Element;
+ import org.w3c.dom.NodeList;
+
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java
+@@ -31,8 +31,8 @@
+ import javax.xml.parsers.DocumentBuilderFactory;
+ import javax.xml.parsers.ParserConfigurationException;
+
+-import org.apache.logging.log4j.LogManager;
+-import org.apache.logging.log4j.Logger;
++import org.apache.log4j.LogManager;
++import org.apache.log4j.Logger;
+ import org.w3c.dom.Document;
+ import org.w3c.dom.Node;
+ import org.w3c.dom.NodeList;
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java
+@@ -28,8 +28,8 @@
+ import java.util.Set;
+ import java.util.TreeSet;
+
+-import org.apache.logging.log4j.LogManager;
+-import org.apache.logging.log4j.Logger;
++import org.apache.log4j.LogManager;
++import org.apache.log4j.Logger;
+
+ /**
+ * Provides programmatic access to ASTRAL representative sets. See the paper by <a
Added: trunk/packages/biojava4-live/trunk/debian/patches/java8_compatibility.patch
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/java8_compatibility.patch (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/java8_compatibility.patch 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,13 @@
+Description: Fix a test failure with Java 8
+Author: Emmanuel Bourg <ebourg at apache.org>
+Forwarded: no
+--- a/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
++++ b/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
+@@ -108,7 +108,7 @@
+ this.circular = circular;
+ this.betweenCompounds = betweenCompounds;
+ this.accession = accession;
+- this.subLocations = Collections.unmodifiableList(subLocations);
++ this.subLocations = subLocations != null ? Collections.unmodifiableList(subLocations) : Collections.<Location>emptyList();
+ assertLocation();
+ }
Added: trunk/packages/biojava4-live/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/series (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/series 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,2 @@
+fix_itext_class_updates
+use_simple_json
Added: trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,52 @@
+Author: Olivier Sallou <osallou at debian/org>
+Last-Updated: 2013-01-03
+Subject: Some tests use network access
+Description: Remove tests requiring external
+ network access
+Forwarded: yes
+Bug: https://redmine.open-bio.org/issues/3402
+--- a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
++++ b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
+@@ -56,17 +56,7 @@
+ * Method 1: With the GenbankProxySequenceReader
+ */
+ //Try with the GenbankProxySequenceReader
+- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
+- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
+- System.out.println("Sequence" + "(" + proteinSequence.getAccession() + "," + proteinSequence.getLength() + ")=" + proteinSequence.getSequenceAsString().substring(0, 10) + "...");
+-
+- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
+- = new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
+- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
+- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
+- System.out.println("Sequence" + "(" + dnaSequence.getAccession() + "," + dnaSequence.getLength() + ")=" + dnaSequence.getSequenceAsString().substring(0, 10) + "...");
++ // Skipping it due to network requirements
+ /*
+ * Method 2: With the GenbankReaderHelper
+ */
+--- a/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
++++ b/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
+@@ -43,21 +43,6 @@
+
+ public void testUniprot(String uniprotID) throws Exception{
+
+- ProteinSequence seq = getUniprot(uniprotID);
+-
+- AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+-
+-/* for (AminoAcidCompound compound : seq) {
+- System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
+- }
+- */
+- compoundSet.verifySequence(seq);
+-
+-
+-
+- @SuppressWarnings("unused")
+- float[] values = Jronn.getDisorderScores(seq);
+-
+
+ }
+
Added: trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,55 @@
+Subject: use simple_json library
+Author: Olivier Sallou <osallou at debian.org>
+Description: json.org library is not "free", use simple_json
+ library and update according to API
+Last-Updated: 2012-12-02
+
+--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
++++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+@@ -20,8 +20,10 @@
+ */
+ package org.biojava.nbio.ws.hmmer;
+
+-import net.sf.json.JSONArray;
+-import net.sf.json.JSONObject;
++import org.json.simple.JSONArray;
++import org.json.simple.JSONObject;
++import org.json.simple.JSONValue;
++
+ import org.biojava.nbio.core.sequence.ProteinSequence;
+
+ import java.io.*;
+@@ -118,15 +120,13 @@
+
+ SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
+ try {
+- JSONObject json = JSONObject.fromObject(result.toString());
+-
+- JSONObject hmresults = json.getJSONObject("results");
+-
++ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
++ JSONObject hmresults = (JSONObject) json.get("results");
+
+- JSONArray hits = hmresults.getJSONArray("hits");
++ JSONArray hits = (JSONArray) hmresults.get("hits");
+
+ for(int i =0 ; i < hits.size() ; i++){
+- JSONObject hit = hits.getJSONObject(i);
++ JSONObject hit = (JSONObject) hits.get(i);
+ //System.out.println("hit: "+ hit);
+
+ HmmerResult hmmResult = new HmmerResult();
+@@ -150,11 +150,11 @@
+ hmmResult.setPvalue((Double)hit.get("pvalue"));
+ hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
+
+- JSONArray hmmdomains = hit.getJSONArray("domains");
++ JSONArray hmmdomains = (JSONArray) hit.get("domains");
+
+ SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
+ for ( int j= 0 ; j < hmmdomains.size() ; j++){
+- JSONObject d = hmmdomains.getJSONObject(j);
++ JSONObject d = (JSONObject) hmmdomains.get(j);
+ //System.out.println(d);
+ Integer is_reported = getInteger(d.get("is_reported"));
+ if ( is_reported != 1) {
Added: trunk/packages/biojava4-live/trunk/debian/rules
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/rules (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/rules 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,81 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_configure:
+ dh_auto_configure
+ sed -e 's/BJLIB/biojava-forester/g' debian/build.xml > biojava-forester/build.xml
+ sed -e 's/BJLIB/biojava-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml
+ sed -e 's/BJLIB/biojava-core/g' debian/build.xml > biojava-core/build.xml
+ sed -e 's/BJLIB/biojava-alignment/g' debian/build.xml > biojava-alignment/build.xml
+ sed -e 's/BJLIB/biojava-genome/g' debian/build.xml > biojava-genome/build.xml
+ sed -e 's/BJLIB/biojava-modfinder/g' debian/build.xml > biojava-modfinder/build.xml
+ sed -e 's/BJLIB/biojava-phylo/g' debian/build.xml > biojava-phylo/build.xml
+ sed -e 's/BJLIB/biojava-sequencing/g' debian/build.xml > biojava-sequencing/build.xml
+ sed -e 's/BJLIB/biojava-protein-disorder/g' debian/build.xml > biojava-protein-disorder/build.xml
+ sed -e 's/BJLIB/biojava-structure/g' debian/build.xml > biojava-structure/build.xml
+ sed -e 's/BJLIB/biojava-ws/g' debian/build.xml > biojava-ws/build.xml
+ sed -e 's/BJLIB/biojava-structure-gui/g' debian/build.xml > biojava-structure-gui/build.xml
+
+override_dh_auto_build:
+ cd biojava-forester && ant jar
+ cd biojava-core && ant jar
+ cd biojava-phylo && ant jar
+ cd biojava-alignment && ant jar
+ cd biojava-aa-prop && ant jar
+ cd biojava-genome && ant jar
+ cd biojava-sequencing && ant jar
+ cd biojava-structure && ant jar
+# cd biojava-structure-gui && ant jar
+ cd biojava-modfinder && ant jar
+ cd biojava-protein-disorder && ant jar
+ cd biojava-ws && ant jar
+ # make doc
+ rm -rf biojavadoc
+ mkdir biojavadoc
+ cp -r biojava-*/src biojavadoc/
+ sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
+ cd biojavadoc && ant javadocs
+ rm -rf biojavadoc
+
+override_dh_auto_test:
+ cd biojava-core && ant test
+ cd biojava-alignment && ant test
+ cd biojava-aa-prop && ant test
+ # Skip, missing dependency
+ #cd biojava-genome && ant test
+ cd biojava-phylo && ant test
+ # Native errors may cause issue on NFS...; skipping
+ #cd biojava-sequencing && ant test
+ #cd biojava-modfinder && ant test
+ cd biojava-protein-disorder && ant test
+ # Requires remote access and tmp directory write access
+ #cd biojava-structure && ant test
+ cd biojava-structure-gui && ant test
+ #No test in biojava-ws available
+ #cd biojava-ws && ant test
+
+
+
+
+override_dh_clean:
+ dh_clean
+ rm -rf build
+ rm -rf dist
+ rm -rf javadoc
+ rm -rf test
+ rm -f biojava-*/build.xml
+ rm -rf biojavadoc
+ rm -rf doc
+
+
+get-orig-source:
+ debian/get-orig-source
+
Property changes on: trunk/packages/biojava4-live/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/biojava4-live/trunk/debian/source/format
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/source/format (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/source/format 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/biojava4-live/trunk/debian/watch
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/watch (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/watch 2015-01-30 21:17:39 UTC (rev 18647)
@@ -0,0 +1,6 @@
+version=3
+
+#opts=filenamemangle=s/.+\/biojava-?(\d\S*)\.tar\.gz/biojava-$1.tar.gz/ \
+opts=dversionmangle=s/\+(repack|dfsg)// \
+ https://github.com/biojava/biojava/tags .*/biojava-?(\d\S*)\.tar\.gz
+
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