[med-svn] r3296 - in trunk/packages/biojava/trunk/debian: . patches
Steffen Möller
smoe-guest at alioth.debian.org
Sun Apr 19 20:58:26 UTC 2009
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 <moeller at debian.org> 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 <moeller at debian.org> Tue, 03 Jul 2007 01:51:06 +0200
+ -- Steffen Moeller <moeller at debian.org> 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 <moeller at debian.org> 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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
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 .. ; \
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