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 <moeller@debian.org>  Sun, 19 Apr 2009 20:52:50 +0200
