[med-svn] r3560 - trunk/packages/biojava/trunk/debian

[Andreas Tille]

Author: tille
Date: 2009-06-26 13:45:28 +0000 (Fri, 26 Jun 2009)
New Revision: 3560

Modified:
   trunk/packages/biojava/trunk/debian/changelog
   trunk/packages/biojava/trunk/debian/control
   trunk/packages/biojava/trunk/debian/copyright
   trunk/packages/biojava/trunk/debian/rules
Log:
Make sure biojava installs nicely over previous versions; fixed clean target by setting JAVA_HOME properly; fixed some lintian issues


Modified: trunk/packages/biojava/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava/trunk/debian/changelog	2009-06-26 13:19:58 UTC (rev 3559)
+++ trunk/packages/biojava/trunk/debian/changelog	2009-06-26 13:45:28 UTC (rev 3560)
@@ -1,3 +1,14 @@
+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 <tille at debian.org>  Fri, 26 Jun 2009 10:01:10 +0200
+
 biojava-live (1.7.svn.20090419-2) unstable; urgency=low
 
   * Add Build Depends: ant-optional

Modified: trunk/packages/biojava/trunk/debian/control
===================================================================
--- trunk/packages/biojava/trunk/debian/control	2009-06-26 13:19:58 UTC (rev 3559)
+++ trunk/packages/biojava/trunk/debian/control	2009-06-26 13:45:28 UTC (rev 3560)
@@ -8,8 +8,9 @@
 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, junit4
-Build-Depends: debhelper, quilt, cdbs, ant, ant-optional
+ openjdk-6-jdk|sun-java6-jdk|sun-java5-jdk|sun-j2sdk1.4|java2-compiler, junit4,
+ ant-optional
+Build-Depends: debhelper, quilt, cdbs, ant
 Standards-Version: 3.8.2
 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/
@@ -19,6 +20,8 @@
 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
+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
@@ -31,6 +34,8 @@
 Package: libbiojava-java
 Architecture: all
 Depends: libbiojava1.7-java
+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
@@ -49,8 +54,10 @@
  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
 Recommends: libbiojava-java
@@ -66,4 +73,5 @@
 Recommends: konqueror|html-browser
 Suggests: libbiojava-java-demos, libbiojava-java
 Description: [Biology] Documentation for BioJava
- JavaDoc generated HTML files describing the API.
+ This package contains the HTML documentation describing the API of BioJava
+ which was generated automatically by JavaDoc.

Modified: trunk/packages/biojava/trunk/debian/copyright
===================================================================
--- trunk/packages/biojava/trunk/debian/copyright	2009-06-26 13:19:58 UTC (rev 3559)
+++ trunk/packages/biojava/trunk/debian/copyright	2009-06-26 13:45:28 UTC (rev 3560)
@@ -87,8 +87,8 @@
  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 
 
-The Debian packaging is (C) 2007-2008, Steffen Moeller <moeller at debian.org> and
-is licensed under the GNU Lesser General Public License version 2.1 or higher,
+The Debian packaging is Copyright 2007-2008, Steffen Moeller <moeller at debian.org>
+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+

Modified: trunk/packages/biojava/trunk/debian/rules
===================================================================
--- trunk/packages/biojava/trunk/debian/rules	2009-06-26 13:19:58 UTC (rev 3559)
+++ trunk/packages/biojava/trunk/debian/rules	2009-06-26 13:45:28 UTC (rev 3560)
@@ -11,6 +11,8 @@
 # in this debian/rules file.
 include /usr/share/cdbs/1/rules/buildvars.mk
 
+export JAVA_HOME := $(shell /usr/sbin/update-java-alternatives -l | head -1 | cut -d' ' -f 3)
+
 # take the first two version numbers to prepare a symbolic link
 # to the real jar
 SOVERSION=$(shell dpkg-parsechangelog | grep ^Version | cut -f2 -d\  |  dpkg-parsechangelog | grep ^Version | cut -f2 -d\   | cut -f1 -d- | cut -f1,2 -d. )