Author: smoe-guest Date: 2009-04-19 20:58:25 +0000 (Sun, 19 Apr 2009) New Revision: 3296
Added: trunk/packages/biojava/trunk/debian/libbiojava1.7-java.dirs Removed: trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs Modified: trunk/packages/biojava/trunk/debian/ trunk/packages/biojava/trunk/debian/README.Debian trunk/packages/biojava/trunk/debian/README.source trunk/packages/biojava/trunk/debian/changelog trunk/packages/biojava/trunk/debian/compat trunk/packages/biojava/trunk/debian/control trunk/packages/biojava/trunk/debian/patches/buildxml.patch trunk/packages/biojava/trunk/debian/rules Log: Update biojava from 1.6 to 1.7, removed libjgrapht-bits and hence the dependency bits that are preventing the adoption by main. Property changes on: trunk/packages/biojava/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Modified: trunk/packages/biojava/trunk/debian/README.Debian =================================================================== --- trunk/packages/biojava/trunk/debian/README.Debian 2009-04-17 15:21:34 UTC (rev 3295) +++ trunk/packages/biojava/trunk/debian/README.Debian 2009-04-19 20:58:25 UTC (rev 3296) @@ -2,18 +2,15 @@ ------------------ All the developers of BioJava are thanked for their fine work. Special -thanks go to Colin Hardman, Andreas Prlic and Simon Brocklehurst for -reacting to my request to get a missing license information into one -of their style sheets. +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. +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. -The packages are now all compiled with the OpenJDK, which now qualifies -them for main. However, libjgrapht in the version currently in sid is -still in contrib. This will be changed. But for now, biojava has to go to the -contrib directory, too, for exactly this reason. - -- Steffen Moeller <[email protected]> Tue, 30 Dec 2008 01:12:41 +0100 Modified: trunk/packages/biojava/trunk/debian/README.source =================================================================== --- trunk/packages/biojava/trunk/debian/README.source 2009-04-17 15:21:34 UTC (rev 3295) +++ trunk/packages/biojava/trunk/debian/README.source 2009-04-19 20:58:25 UTC (rev 3296) @@ -23,6 +23,10 @@ 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. @@ -31,6 +35,7 @@ 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. +of your interest at http://pkg-escience.alioth.debian.org and on the +BioJava home page. - -- Steffen Moeller <[email protected]> Tue, 03 Jul 2007 01:51:06 +0200 + -- Steffen Moeller <[email protected]> Sun, 19 Apr 2009 20:52:50 +0200 Modified: trunk/packages/biojava/trunk/debian/changelog =================================================================== --- trunk/packages/biojava/trunk/debian/changelog 2009-04-17 15:21:34 UTC (rev 3295) +++ trunk/packages/biojava/trunk/debian/changelog 2009-04-19 20:58:25 UTC (rev 3296) @@ -1,3 +1,11 @@ +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 <[email protected]> Sun, 19 Apr 2009 18:30:54 +0200 + biojava-live (1.6.1.svn.20090306-2) UNRELEASED; urgency=low TODO: do not miss the relicensing of @@ -4,6 +12,8 @@ tests/org/biojava/utils/process/AllTests.java in the next upstream version (see http://bugzilla.open-bio.org/show_bug.cgi?id=2797) + Update: done, upstream has addressed this (Steffen, 4/09) + -- Andreas Tille <[email protected]> Tue, 24 Mar 2009 08:45:50 +0100 biojava-live (1.6.1.svn.20090306-1) experimental; urgency=low Modified: trunk/packages/biojava/trunk/debian/compat =================================================================== --- trunk/packages/biojava/trunk/debian/compat 2009-04-17 15:21:34 UTC (rev 3295) +++ trunk/packages/biojava/trunk/debian/compat 2009-04-19 20:58:25 UTC (rev 3296) @@ -1 +1 @@ -4 +5 Modified: trunk/packages/biojava/trunk/debian/control =================================================================== --- trunk/packages/biojava/trunk/debian/control 2009-04-17 15:21:34 UTC (rev 3295) +++ trunk/packages/biojava/trunk/debian/control 2009-04-19 20:58:25 UTC (rev 3296) @@ -1,5 +1,5 @@ Source: biojava-live -Section: contrib/science +Section: science Priority: optional Maintainer: Debian-Med Packaging Team <[email protected]> DM-Upload-Allowed: yes @@ -8,15 +8,14 @@ Build-Depends-Indep: libcommons-cli-java, libcommons-dbcp-java (>= 1.1), libhsqldb-java, libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1), libbytecode-java (>= 0.92.cvs.20070925), - openjdk-6-jdk|sun-java6-jdk|sun-java5-jdk|sun-j2sdk1.4|java2-compiler, ant, junit4, - libjgrapht0.7-java|libjgrapht-java (>=0.7) -Build-Depends: debhelper, quilt -Standards-Version: 3.8.0 + openjdk-6-jdk|sun-java6-jdk|sun-java5-jdk|sun-j2sdk1.4|java2-compiler, junit4 +Build-Depends: debhelper, quilt, cdbs, ant +Standards-Version: 3.8.1 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: libbiojava1.6-java +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, openjdk-6-jre|sun-java6-jre|sun-java5-jre|java2-runtime Suggests: java-virtual-machine, libjgrapht-java, libbiojava-java, libbiojava-java-doc @@ -31,7 +30,7 @@ Package: libbiojava-java Architecture: all -Depends: libbiojava1.6-java +Depends: libbiojava1.7-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 @@ -62,7 +61,7 @@ Package: libbiojava-java-doc -Section: contrib/doc +Section: doc Architecture: all Recommends: konqueror|html-browser Suggests: libbiojava-java-demos, libbiojava-java Deleted: trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs =================================================================== --- trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs 2009-04-17 15:21:34 UTC (rev 3295) +++ trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs 2009-04-19 20:58:25 UTC (rev 3296) @@ -1 +0,0 @@ -usr/share/java Copied: trunk/packages/biojava/trunk/debian/libbiojava1.7-java.dirs (from rev 3295, trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs) =================================================================== --- trunk/packages/biojava/trunk/debian/libbiojava1.7-java.dirs (rev 0) +++ trunk/packages/biojava/trunk/debian/libbiojava1.7-java.dirs 2009-04-19 20:58:25 UTC (rev 3296) @@ -0,0 +1 @@ +usr/share/java Modified: trunk/packages/biojava/trunk/debian/patches/buildxml.patch =================================================================== --- trunk/packages/biojava/trunk/debian/patches/buildxml.patch 2009-04-17 15:21:34 UTC (rev 3295) +++ trunk/packages/biojava/trunk/debian/patches/buildxml.patch 2009-04-19 20:58:25 UTC (rev 3296) @@ -1,5 +1,5 @@ ---- biojava-live-1.6.svn.20080713.orig/build.xml -+++ biojava-live-1.6.svn.20080713/build.xml +--- biojava-live-1.7.svn.20090419.orig/build.xml ++++ biojava-live-1.7.svn.20090419/build.xml @@ -51,7 +51,7 @@ <tstamp /> <property name="version" value="live" /> @@ -18,7 +18,7 @@ <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; offline="false"/> <group title="Core biological packages" -@@ -464,7 +464,7 @@ +@@ -465,7 +465,7 @@ source="1.5" windowtitle="${Name.demos} API" doctitle="${Name.demos}" @@ -27,7 +27,7 @@ <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; offline="false"/> <link href="../biojava" offline="true" packagelistLoc="${build.docs.biojava}/package-list}"/> </javadoc> -@@ -485,7 +485,7 @@ +@@ -486,7 +486,7 @@ source="1.5" windowtitle="${Name.apps} API" doctitle="${Name.apps}" @@ -36,7 +36,7 @@ <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; offline="false"/> <link href="../biojava" offline="true" packagelistLoc="${build.docs.biojava}/package-list}"/> -@@ -507,7 +507,7 @@ +@@ -508,7 +508,7 @@ description="Run all tests, can be quite slow"> <property name="test.subtree" value="**" /> <echo message="Running tests: ${test.subtree}" /> @@ -45,7 +45,7 @@ <formatter type="plain" usefile="true" /> <classpath> <!-- main classes from build --> -@@ -547,7 +547,7 @@ +@@ -548,7 +548,7 @@ classpath="${classpath}" destdir="${build.doccheck.biojava}" source="1.5" @@ -54,7 +54,7 @@ </javadoc> </target> -@@ -558,7 +558,7 @@ +@@ -559,7 +559,7 @@ description="Run clean, build and tests for CruiseControl"> <property name="test.subtree" value="**" /> <echo message="Running tests: ${test.subtree}" /> Modified: trunk/packages/biojava/trunk/debian/rules =================================================================== --- trunk/packages/biojava/trunk/debian/rules 2009-04-17 15:21:34 UTC (rev 3295) +++ trunk/packages/biojava/trunk/debian/rules 2009-04-19 20:58:25 UTC (rev 3296) @@ -4,13 +4,27 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 +# include macros on how to deal with quilt include /usr/share/quilt/quilt.make +# include series of variables to become more version-independent +# in this debian/rules file. +include /usr/share/cdbs/1/rules/buildvars.mk + +# take the first two version numbers to prepare a symbolic link +# to the real jar +SOVERSION=$(shell dpkg-parsechangelog | grep ^Version | cut -f2 -d\ | dpkg-parsechangelog | grep ^Version | cut -f2 -d\ | cut -f1 -d- | 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 @@ -34,7 +48,7 @@ dh_clean -k dh_installdirs - cp ant-build/biojava.jar $(CURDIR)/debian/libbiojava1.6-java/usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar + 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/* $$d @@ -58,7 +72,7 @@ dh_installexamples -plibbiojava-java-demos demos/* #dh_installman dh_link -p libbiojava-java /usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar /usr/share/java/biojava.jar - dh_link -p libbiojava1.6-java /usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar /usr/share/java/biojava1.6.jar + dh_link -p libbiojava$(SOVERSION)-java /usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar /usr/share/java/biojava$(SOVERSION).jar dh_link # use <pkg>.link files for version independant linking dh_compress dh_fixperms @@ -70,7 +84,7 @@ binary: binary-indep binary-arch get-orig-source: - version=1.6.1.svn.`date +"%Y%m%d"|tr -d '\n'` ; \ + version=$(DEB_UPSTREAM_VERSION).svn.`date +"%Y%m%d"|tr -d '\n'` ; \ targetdir=biojava-live-$$version ; \ origtargz=biojava-live_$$version.orig.tar.gz ; \ cd .. ; \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
