--- biojava-live-1.7.1.orig/debian/control +++ biojava-live-1.7.1/debian/control @@ -0,0 +1,79 @@ +Source: biojava-live +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller , + Andreas Tille +Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java, + libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1), + libbytecode-java (>= 0.92.cvs.20070925), + default-jdk-builddep|openjdk-6-jdk|sun-java6-jdk|sun-java5-jdk|sun-j2sdk1.4|java2-compiler, junit4, + ant-optional +Build-Depends: debhelper (>= 5), quilt, cdbs, ant +Standards-Version: 3.8.3 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/biojava/trunk/ +Homepage: http://www.biojava.org + +Package: libbiojava1.7-java +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, libcommons-pool-java (>= 1.1), libcommons-collections-java (>= 2.1), libcommons-dbcp-java (>= 1.1), libhsqldb-java, libbytecode-java, default-jre-headless|openjdk-6-jre|sun-java6-jre|sun-java5-jre|java2-runtime +Suggests: java-virtual-machine, libjgrapht-java, libbiojava-java, libbiojava-java-doc +Conflicts: libbiojava1.6-java +Replaces: libbiojava1.6-java +Description: Java API to biological data and applications + This package presents the Open Source Java API to biological databases + and a series of mostly sequence-based algorithms. The APIs are not + compatible between versions. In analogy to the dealing with shared + libraries of the C language, the jar file of this package has the + API version in its name. It is symbolically linked to the expected + biojava.jar filename in the package libbiojava-java. This will help + keeping multiple versions of the biojava API in parallel. + +Package: libbiojava-java +Architecture: all +Depends: libbiojava1.7-java, ${misc:Depends} +Conflicts: libbiojava1.6-java +Replaces: libbiojava1.6-java +Description: Java API to biological data and applications + 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. + . + This is a wrapper package which should enable smooth upgrades to new + versions. + +Package: libbiojava-java-demos +Architecture: all +Depends: ${misc:Depends} +Recommends: libbiojava-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: libbiojava-java-doc +Section: doc +Architecture: all +Depends: ${misc:Depends} +Recommends: konqueror|html-browser +Suggests: libbiojava-java-demos, libbiojava-java +Description: [Biology] Documentation for BioJava + This package contains the HTML documentation describing the API of BioJava + which was generated automatically by JavaDoc. --- biojava-live-1.7.1.orig/debian/compat +++ biojava-live-1.7.1/debian/compat @@ -0,0 +1 @@ +5 --- biojava-live-1.7.1.orig/debian/copyright +++ biojava-live-1.7.1/debian/copyright @@ -0,0 +1,100 @@ +This package was debianized by Steffen Moeller on +Wed, 31 Dec 2008 01:26:45 +0100 + +It was downloaded from http://www.biojava.org/download/source + +Copyright: 1999-2008 the Individual authors who contributed the code, + as identified by the @authors tag of the respective source file. + +Upstream Authors: BioJava Developers + Namely: Alan Li, Andreas Dräger , Andreas Prlic, + Andy Hammer, Andy Yates, Andy Yates, Aroul Ramadass, Bradford Powell, + Brian Gilman, Brian King, Bubba Puryear, Colin Hardman , David Allen, + David H. Klatte, David Huen, David Scott, David Waring, Eric Haugen, + Ewan Birney, Francois Pepin, Frans Verhoef, Frederik Decouttere, Gerald + Loeffler , Greg Cox, G. Waldon, Hanning + Ni ,, Horvath Tamas, Jason Stajich, Jim Balhoff, John Day Richter, + Jolyon Holdstock, Jonathan Warren, Jules Jacobsen, Kalle Naslund, + Keith James , Lachlan Coin, Laurent Jourdren, Leen + Ammeraal, Lei Lai, Len Trigg, Lorna Morris, Lukas Kall, Mark Schreiber + , Mark Southern, Markus Brosch, Martin + Senger , Martin Szugat , Mathew + Pocock, Mathieu Wiepert , Matthew Pocock, Mayo Foundation, Michael Heuer, + Michael Jones, Michael L Heurer, Mike Jones, Moses Hohman, Nimesh Singh, + Paul Seed, Peter Lackner, raemig, Rahul Karnik, Rhett Sutphin, Richard + Holland, Ronald Tschalar, Ron Kuhn, Russell Smithies, Samiul Hasan, + Shuvankar Mukherjee, Simon Brocklehurst, Simon Foote, Stuart Johnston , + Susanne Merz, Tamas Horvath, Tanya Vavouri, Thad Welch, Thomas Down, + Tim Dilks , Tobias Thierer, Todd Riley + + +License: LGPL-2.1+ + + BioJava is an open source project. The project is distributed under the GNU + Lesser General Public Licence. We do not consider Java class loading to + constitute the production of a derivative work. We do not consider consider + sub-classing of Java classes or implementations of Java interfaces to constitute + the production of a derivative work. + + All .java source files should include the following comment which implies the + author's agreement to the tearms of the license. + + /* + * BioJava development code + * + * This code may be freely distributed and modified under the + * terms of the GNU Lesser General Public Licence. This should + * be distributed with the code. If you do not have a copy, + * see: + * + * http://www.gnu.org/copyleft/lesser.html + * + * Copyright for this code is held jointly by the individual + * authors. These should be listed in @author doc comments. + * + * For more information on the BioJava project and its aims, + * or to join the biojava-l mailing list, visit the home page + * at: + * + * http://www.biojava.org/ + * + */ + + 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 + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this package; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + +File: /tests/org/biojava/utils/process/AllTests.java +Copyright: © 2005, BioWeka.org +License: GPL-2+ + 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + + +The Debian packaging is Copyright 2007-2008, Steffen Moeller +and is licensed under the GNU Lesser General Public License version 2.1 or higher, +see `/usr/share/common-licenses/LGPL-2.1'. + +License: LGPL-2.1+ + On Debian systems, the complete text of the GNU Lesser General Public License + version 2.1 can be found in `/usr/share/common-licenses/LGPL-2.1'. + +License: GPL-2+ + On Debian systems, the complete text of the GNU General Public License + version 2 can be found in `/usr/share/common-licenses/GPL-2'. --- biojava-live-1.7.1.orig/debian/rules +++ biojava-live-1.7.1/debian/rules @@ -0,0 +1,103 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +# include macros on how to deal with quilt +include /usr/share/quilt/quilt.make + +# include series of variables to become more version-independent +# in this debian/rules file. +include /usr/share/cdbs/1/rules/buildvars.mk + +export JAVA_HOME := $(shell /usr/sbin/update-java-alternatives -l | head -1 | cut -d' ' -f 3) + +# version are the first two decimals +SOVERSION=$(shell echo $(DEB_UPSTREAM_VERSION) | cut -f1,2 -d. ) + +build: patch build-stamp + +build-stamp: + dh_testdir + find . -name "*.java" -o -name ReadMe -o -name "*.fa" -o -name "*.html" | xargs -r chmod 644 + # circumvent Debian's difficulties with libjgrapht - deleting all usage of that library + rm -rf src/org/biojavax/bio/phylo/io/nexus/ \ + src/org/biojavax/bio/phylo/DistanceBasedTreeMethod.java \ + src/org/biojavax/bio/phylo/ParsimonyTreeMethod.java + + # Add here commands to compile the package. + ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava + #ant compile-demos + ant javadocs-biojava + + touch build-stamp + +clean: unpatch + dh_testdir + dh_testroot + rm -f build-stamp + + # Add here commands to clean up after the build process. + ant clean + + dh_clean + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + + cp ant-build/biojava.jar $(CURDIR)/debian/libbiojava$(SOVERSION)-java/usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar + d=$(CURDIR)/debian/libbiojava-java-doc/usr/share/doc/libbiojava-java/api; \ + [ -d $$d ] || mkdir -p $$d ; \ + cp -r ant-build/docs/biojava/* $$d + for i in $(CURDIR)/debian/libbiojava-java*; do \ + if [ -d "$i" ]; then \ + find $i -name ".svn" | xargs -r rm -r ; \ + fi ; \ + done + + ant runtests + + +binary-arch: +# We have nothing to do by default. + +binary-indep: build install + dh_testdir + dh_testroot + dh_installchangelogs + dh_installdocs + dh_installexamples -plibbiojava-java-demos demos/* + #dh_installman + dh_link -p libbiojava-java /usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar /usr/share/java/biojava.jar + # thinking about svn snapshots + if [ "$(SOVERSION)" != "$(DEB_UPSTREAM_VERSION)" ]; then \ + dh_link -p libbiojava$(SOVERSION)-java \ + /usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar \ + /usr/share/java/biojava$(SOVERSION).jar; \ + fi + dh_link # use .link files for version independant linking + dh_compress + dh_fixperms + dh_installdeb + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch + +get-orig-source: + version=$(DEB_UPSTREAM_VERSION).svn.`date +"%Y%m%d"|tr -d '\n'` ; \ + targetdir=biojava-live-$$version ; \ + origtargz=biojava-live_$$version.orig.tar.gz ; \ + cd .. ; \ + svn co svn://code.open-bio.org/biojava/biojava-live/trunk $$targetdir ; \ + find $$targetdir -name ".svn" | xargs -r rm -r ; \ + find $$targetdir -name "*.jar" | xargs -r rm ; \ + tar czf $$origtargz $$targetdir ; \ + rm -rf $$targetdir + +.PHONY: build clean binary-indep binary-arch binary install configure get-orig-source --- biojava-live-1.7.1.orig/debian/libbiojava-java-doc.dirs +++ biojava-live-1.7.1/debian/libbiojava-java-doc.dirs @@ -0,0 +1 @@ +usr/share/doc/libbiojava-java --- biojava-live-1.7.1.orig/debian/changelog +++ biojava-live-1.7.1/debian/changelog @@ -0,0 +1,64 @@ +biojava-live (1:1.7.1-1) unstable; urgency=low + + * New upstream version. + * New epoch + - because of an unfortunate versioning of previous upload + - to indicate the now happening BioJava Hackathon in Cambridge, UK + + -- Steffen Moeller Wed, 20 Jan 2010 02:08:17 +0100 + +biojava-live (1.7.svn.20090419-3) unstable; urgency=low + + * debian/control: + - Conflicts: libbiojava1.6-java + - Replaces: libbiojava1.6-java + - Enhanced long description of libbiojava-java-doc + Closes: #522269 + * debian/rules: set JAVA_HOME to enable proper clean target + + -- Andreas Tille Fri, 26 Jun 2009 10:01:10 +0200 + +biojava-live (1.7.svn.20090419-2) unstable; urgency=low + + * Add Build Depends: ant-optional + Closes: #533896 + * Standards-Version: 3.8.2 (no changes needed) + + -- Andreas Tille Mon, 22 Jun 2009 09:32:20 +0200 + +biojava-live (1.7.svn.20090419-1) unstable; urgency=low + + * New upstream version, addressing structures. + * Removed dependency on libjgrapht, so biojava can go to main. + * Conformance to 3.8.1 (no changes required). + + -- Steffen Moeller Sun, 19 Apr 2009 18:30:54 +0200 + +biojava-live (1.6.1.svn.20090306-1) experimental; urgency=low + + [ Andreas Tille ] + * Initial release (Closes:#491025). + + [ Steffen Moeller ] + * Added dependency to quilt. + * Moved -doc to section doc. + * Added symlinks to jar file with pseudo-soname + * Need to be placed in contrib section as a start because of dependency + to libjgrapht that is still in contrib. + + -- Andreas Tille Mon, 09 Mar 2009 13:50:45 +0100 + +biojava-live (1.6.0.svn.20080716-1) UNRELEASED; urgency=low + + * Renamed to biojava-live in analogy to upstream's name + and to keep the opportunity to add a biojava meta package + later on. + * License issue fixed that led to previous rejection of biojava. + + -- Steffen Moeller Sun, 13 Jul 2008 15:56:27 +0200 + +biojava (1.5-1) UNRELEASED; urgency=low + + * New upstream release. + + -- Steffen Moeller Tue, 03 Jul 2007 01:51:06 +0200 --- biojava-live-1.7.1.orig/debian/watch +++ biojava-live-1.7.1/debian/watch @@ -0,0 +1,5 @@ +version=3 +# Well, this only finds updates to version 1.5 +#http://www.biojava.org/download/bj15/src/BioJava(.*)-src.tar.gz +# offers no source +http://www.biojava.org/download/bj171/src/biojava-(.*)-src.jar --- biojava-live-1.7.1.orig/debian/README.source +++ biojava-live-1.7.1/debian/README.source @@ -0,0 +1,41 @@ +biojava for Debian +------------------ + +The following jars from the upstream source distribution were +substituted by Debian packages: + + bytecode.jar + commons-cli.jar + commons-collections-2.1.jar + commons-dbcp-1.1.jar + commons-pool-1.1.jar + jgrapht-jdk1.5.jar + junit-4.4.jar + +These libraries are very common (well, this probably is why they are +named this way) and hence changes in their API very likely to effect many +programs. Nevertheless, without a proper management of Java archives +in Debian, i.e., by raven/maven, it is somewhat conflict-prone to use +other Jars than the ones deployed with upstream sources. + +Exceptions is bytecode.jar which is developed by the BioJava community +and is hence always strongly coupled to this package. The jgrapht library +underwent a recent change in its API and is hence incompatible with +the latest release. + +The source code fiddling with jgrapht is still shipped, it is only removed +at the time of the compilation. This way, the orig.tar.gz file does not +need to be changed when the situation concerning jgrapht packaging demystifies. + +The documentation was separated from the jar file and so was the huge +demos folder with code examples. + +If indicated as such by the string "svn" in the version string, the +sources were taken directly from the upstream subversion repository +as svn co svn://code.open-bio.org/biojava/biojava-live/trunk biojava-live + +Help to improve the packaging is appreciated. You may find more packages +of your interest at http://pkg-escience.alioth.debian.org and on the +BioJava home page. + + -- Steffen Moeller Sun, 19 Apr 2009 20:52:50 +0200 --- biojava-live-1.7.1.orig/debian/libbiojava-java-doc.doc-base +++ biojava-live-1.7.1/debian/libbiojava-java-doc.doc-base @@ -0,0 +1,26 @@ +Document: biojava +Title: biojava 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 --- biojava-live-1.7.1.orig/debian/libbiojava-java-doc.links +++ biojava-live-1.7.1/debian/libbiojava-java-doc.links @@ -0,0 +1 @@ +usr/share/doc/libbiojava-java/api usr/share/doc/libbiojava-java-doc/api --- biojava-live-1.7.1.orig/debian/libbiojava1.7-java.lintian +++ biojava-live-1.7.1/debian/libbiojava1.7-java.lintian @@ -0,0 +1 @@ +W: libbiojava1.7-java: wrong-section-according-to-package-name --- biojava-live-1.7.1.orig/debian/libbiojava1.7-java.dirs +++ biojava-live-1.7.1/debian/libbiojava1.7-java.dirs @@ -0,0 +1 @@ +usr/share/java --- biojava-live-1.7.1.orig/debian/libbiojava-java.docs +++ biojava-live-1.7.1/debian/libbiojava-java.docs @@ -0,0 +1,4 @@ +README +README.biosql +resources +dtd --- biojava-live-1.7.1.orig/debian/README.Debian +++ biojava-live-1.7.1/debian/README.Debian @@ -0,0 +1,16 @@ +biojava for Debian +------------------ + +All the developers of BioJava are thanked for their fine work. Special +thanks go to Colin Hardman, Andreas Prlic, Simon Brocklehurst and Richard +Holland for reacting to my requests to add missing license information. + +The package is not completely functional because of a dependency of +a very small fraction of code that is of little practical relevance to +the vast majority of BioJava users. This dependes on jgrapht libraries +of version 1.5 that are not in Debian. That fraction is not compiled, +the dependency to jgrapht could hence be removed from the binary so +BioJava goes from contrib/experimental into the main section of the +release. + + -- Steffen Moeller Tue, 30 Dec 2008 01:12:41 +0100 --- biojava-live-1.7.1.orig/debian/libbiojava-java.lintian +++ biojava-live-1.7.1/debian/libbiojava-java.lintian @@ -0,0 +1 @@ +W: libbiojava-java: wrong-section-according-to-package-name --- biojava-live-1.7.1.orig/debian/patches/series +++ biojava-live-1.7.1/debian/patches/series @@ -0,0 +1 @@ +buildxml.patch --- biojava-live-1.7.1.orig/debian/patches/buildxml.patch +++ biojava-live-1.7.1/debian/patches/buildxml.patch @@ -0,0 +1,65 @@ +--- biojava-live-1.7.svn.20090419.orig/build.xml ++++ biojava-live-1.7.svn.20090419/build.xml +@@ -51,7 +51,7 @@ + + + +- ++ + + + +@@ -401,7 +401,7 @@ + source="1.5" + windowtitle="${Name.biojava}-${version} API" + doctitle="${Name.biojava}-${version}" +- maxmemory="96m"> ++ maxmemory="512m"> + + + ++ maxmemory="512m"> + + + +@@ -486,7 +486,7 @@ + source="1.5" + windowtitle="${Name.apps} API" + doctitle="${Name.apps}" +- maxmemory="96m"> ++ maxmemory="512m"> + + + +@@ -508,7 +508,7 @@ + description="Run all tests, can be quite slow"> + + +- ++ + + + +@@ -548,7 +548,7 @@ + classpath="${classpath}" + destdir="${build.doccheck.biojava}" + source="1.5" +- maxmemory="96m"> ++ maxmemory="512m"> + + + +@@ -559,7 +559,7 @@ + description="Run clean, build and tests for CruiseControl"> + + +-