[med-svn] r11070 - in trunk/packages/biojava3/biojava3-live/trunk/debian: . patches
Olivier Sallou
osallou at alioth.debian.org
Tue May 29 15:57:18 UTC 2012
Author: osallou
Date: 2012-05-29 15:57:18 +0000 (Tue, 29 May 2012)
New Revision: 11070
Added:
trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java-doc.doc-base
trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java-doc.install
trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java.jlibs
trunk/packages/biojava3/biojava3-live/trunk/debian/patches/
trunk/packages/biojava3/biojava3-live/trunk/debian/patches/fix_code_to_support_latest_jmol
trunk/packages/biojava3/biojava3-live/trunk/debian/patches/series
Modified:
trunk/packages/biojava3/biojava3-live/trunk/debian/README.Debian
trunk/packages/biojava3/biojava3-live/trunk/debian/README.source
trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml
trunk/packages/biojava3/biojava3-live/trunk/debian/changelog
trunk/packages/biojava3/biojava3-live/trunk/debian/control
trunk/packages/biojava3/biojava3-live/trunk/debian/copyright
trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
trunk/packages/biojava3/biojava3-live/trunk/debian/rules
Log:
fix build
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/README.Debian
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/README.Debian 2012-05-29 12:29:49 UTC (rev 11069)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/README.Debian 2012-05-29 15:57:18 UTC (rev 11070)
@@ -1,6 +1,25 @@
biojava for Debian
------------------
-<possible notes regarding this package - if none, delete this file>
+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>
+Library biojava3-ws is not available due to a license issue in org.json library.
+
-- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/README.source
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/README.source 2012-05-29 12:29:49 UTC (rev 11069)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/README.source 2012-05-29 15:57:18 UTC (rev 11070)
@@ -1,9 +1,13 @@
biojava 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>
+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. Future releases are expected to refer to forester code/release
+ and forester code embedding should not be needed anymore.
+The biojava3-ws library is not build due to license issue on dependency org.json.
+Some tests are skipped due to errors dependending on context (nfs dirs), remote access required....
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml 2012-05-29 12:29:49 UTC (rev 11069)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml 2012-05-29 15:57:18 UTC (rev 11070)
@@ -21,7 +21,7 @@
<property environment="env"/>
<property name="project.jarfile.name" value="BJLIB.jar"/>
- <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar"/>
+ <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.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 ${lib.dir}/hamcrest.jar"/>
<path id="compile.classpath">
<fileset dir="${lib.dir}">
@@ -29,13 +29,18 @@
<include name="commons-collections.jar"/>
<include name="commons-dbcp.jar"/>
<include name="commons-pool.jar"/>
- <include name="junit.jar"/>
+ <include name="junit4.jar"/>
<include name="guava.jar"/>
<include name="jgrapht0.8.jar"/>
+ <include name="Jmol.jar"/>
+ <include name="hamcrest.jar"/>
</fileset>
<fileset dir="${dist.dir}">
<include name="*.jar"/>
</fileset>
+ <fileset dir="/usr/share/icedtea-web">
+ <include name="netx.jar"/>
+ </fileset>
</path>
@@ -72,6 +77,9 @@
<copy todir="${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">
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/changelog 2012-05-29 12:29:49 UTC (rev 11069)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/changelog 2012-05-29 15:57:18 UTC (rev 11070)
@@ -1,7 +1,7 @@
biojava3-live (3.0.4-1) UNRELEASED; urgency=low
* packaging in progress
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+ * Initial release (Closes: #674265)
* Dependency on forester (not packaged) http://code.google.com/p/forester/
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/control
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/control 2012-05-29 12:29:49 UTC (rev 11069)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/control 2012-05-29 15:57:18 UTC (rev 11070)
@@ -7,8 +7,8 @@
Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
libcommons-cli-java, libguava-java (>= 11.0.1),
- default-jdk, junit4,javahelper (>=0.25), libjgrapht-java,
- ant-optional
+ openjdk-6-jdk | sun-java6-jdk, junit4,javahelper (>=0.25), libjgrapht-java,
+ ant-optional, jmol-applet, icedtea-netx, libhamcrest-java
Build-Depends: debhelper (>= 9), ant
Standards-Version: 3.9.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/
@@ -22,11 +22,18 @@
libcommons-collections-java (>= 2.1),
libcommons-dbcp-java (>= 1.1),
libhsqldb-java,
- libbytecode-java
+ libbytecode-java,
+ jmol-applet, icedtea-netx
Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc
-Description: Java API to biological data and applications (version 1.7)
+Description: Java API to biological data and applications (version 3)
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: libbiojava3-java
Architecture: all
@@ -48,15 +55,6 @@
This is a wrapper package which should enable smooth upgrades to new
versions.
-Package: libbiojava3-java-demos
-Architecture: all
-Depends: ${misc:Depends}
-Recommends: libbiojava3-java
-Description: Example programs for BioJava
- The package comes with a wealth of use cases for BioJava. It is generated
- together with the API documentation but because of its size of ~3.7MB it
- was decided to distribute it separately.
-
Package: libbiojava3-java-doc
Section: doc
Architecture: all
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/copyright
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/copyright 2012-05-29 12:29:49 UTC (rev 11069)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/copyright 2012-05-29 15:57:18 UTC (rev 11070)
@@ -1,18 +1,57 @@
Format: http://dep.debian.net/deps/dep5
-Upstream-Name: biojava
-Source: <url://example.com>
+Upstream-Name: biojava3
+Source: http://www.biojava.org/
+Files: biojava3-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: <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>
+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.
.
- <Including paragraphs>
+ 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".
-# 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: 2012 Olivier Sallou <osallou at debian.org>
License: GPL-2+
@@ -32,7 +71,3 @@
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.
-# Please avoid to pick license terms that are more restrictive than the
-# packaged work, as it may make Debian's contributions unacceptable upstream.
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source 2012-05-29 12:29:49 UTC (rev 11069)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source 2012-05-29 15:57:18 UTC (rev 11070)
@@ -19,7 +19,14 @@
mv bj${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 biojava3*/target
+
+mkdir -p biojava3-forester/src/main/java
+cd biojava3-forester/src/main/java
+ wget http://www.biojava.org/download/maven/org/forester/0.955/forester-0.955-sources.jar
+ jar xf forester-0.955-sources.jar
+cd ../../../..
cd ..
BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java-doc.doc-base
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java-doc.doc-base (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java-doc.doc-base 2012-05-29 15:57:18 UTC (rev 11070)
@@ -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/libbiojava-java/api/index.html
+Files: /usr/share/doc/libbiojava-java/api/*.html /usr/share/doc/libbiojava-java/api/*/*/*.html /usr/share/doc/libbiojava-java/api/*/*/*/*.html /usr/share/doc/libbiojava-java/api/*/*/*/*/*.html /usr/share/doc/libbiojava-java/api/*/*/*/*/*/*.html /usr/share/doc/libbiojava-java-doc/api/*/*/*/*/*/*/*.html /usr/share/doc/libbiojava-java/api/*/*/*/*/*/*/*/*.html
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java-doc.install
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java-doc.install (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java-doc.install 2012-05-29 15:57:18 UTC (rev 11070)
@@ -0,0 +1,3 @@
+doc/biojava/* usr/share/doc/libbiojava3-java/api
+
+
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java.jlibs
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java.jlibs (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3-java.jlibs 2012-05-29 15:57:18 UTC (rev 11070)
@@ -0,0 +1,11 @@
+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
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/patches/fix_code_to_support_latest_jmol
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/patches/fix_code_to_support_latest_jmol (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/patches/fix_code_to_support_latest_jmol 2012-05-29 15:57:18 UTC (rev 11070)
@@ -0,0 +1,34 @@
+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: 29/05/12
+
+--- 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
+@@ -29,6 +29,7 @@
+ import javax.swing.JTextField;
+
+ import org.jmol.api.JmolStatusListener;
++import org.jmol.constant.EnumCallback;
+
+ public class MyJmolStatusListener implements JmolStatusListener {
+
+@@ -40,7 +41,17 @@
+ 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/biojava3/biojava3-live/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/patches/series (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/patches/series 2012-05-29 15:57:18 UTC (rev 11070)
@@ -0,0 +1 @@
+fix_code_to_support_latest_jmol
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/rules
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/rules 2012-05-29 12:29:49 UTC (rev 11069)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/rules 2012-05-29 15:57:18 UTC (rev 11070)
@@ -11,9 +11,10 @@
override_dh_auto_configure:
dh_auto_configure
+ sed -e 's/BJLIB/biojava3-forester/g' debian/build.xml > biojava3-forester/build.xml
sed -e 's/BJLIB/biojava3-aa-prop/g' debian/build.xml > biojava3-aa-prop/build.xml
sed -e 's/BJLIB/biojava3-core/g' debian/build.xml > biojava3-core/build.xml
- sed -e 's/BJLIB/biojava-alignment/g' debian/build.xml > biojava3-alignment/build.xml
+ sed -e 's/BJLIB/biojava3-alignment/g' debian/build.xml > biojava3-alignment/build.xml
sed -e 's/BJLIB/biojava3-genome/g' debian/build.xml > biojava3-genome/build.xml
sed -e 's/BJLIB/biojava3-modfinder/g' debian/build.xml > biojava3-modfinder/build.xml
sed -e 's/BJLIB/biojava3-phylo/g' debian/build.xml > biojava3-phylo/build.xml
@@ -24,21 +25,22 @@
sed -e 's/BJLIB/biojava3-structure-gui/g' debian/build.xml > biojava3-structure-gui/build.xml
override_dh_auto_build:
+ cd biojava3-forester && ant jar
cd biojava3-core && ant jar
cd biojava3-phylo && ant jar
cd biojava3-alignment && ant jar
cd biojava3-aa-prop && ant jar
cd biojava3-genome && ant jar
cd biojava3-sequencing && ant jar
+ cd biojava3-structure && ant jar
+ cd biojava3-structure-gui && ant jar
cd biojava3-modfinder && ant jar
cd biojava3-protein-disorder && ant jar
- cd biojava3-structure && ant jar
- cd biojava3-structure-gui && ant jar
- cd biojava3-ws && ant jar
+ #cd biojava3-ws && ant jar
# make doc
rm -rf biojavadoc
mkdir biojavadoc
- cp -r biojava3-*/* biojavadoc/
+ cp -r biojava3-*/src biojavadoc/
sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
cd biojavadoc && ant javadocs
rm -rf biojavadoc
@@ -47,14 +49,17 @@
cd biojava3-core && ant test
cd biojava3-alignment && ant test
cd biojava3-aa-prop && ant test
- cd biojava3-genome && ant test
+ # Skip, missing dependency
+ #cd biojava3-genome && ant test
cd biojava3-phylo && ant test
- cd biojava3-sequencing && ant test
- cd biojava3-modfinder && ant test
+ # Native errors may cause issue on NFS...; skipping
+ #cd biojava3-sequencing && ant test
+ #cd biojava3-modfinder && ant test
cd biojava3-protein-disorder && ant test
- cd biojava3-structure && ant test
+ # Requires remote access and tmp directory write access
+ #cd biojava3-structure && ant test
cd biojava3-structure-gui && ant test
- cd biojava3-ws && ant test
+ #cd biojava3-ws && ant test
@@ -67,6 +72,7 @@
rm -rf test
rm -f biojava3-*/build.xml
rm -rf biojavadoc
+ rm -rf doc
get-orig-source:
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