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