ports/110621: [UPDATE]update biojava to 1.5beta2:a Java framework for processing biological data.

[Nemo Liu]

>Number:         110621
>Category:       ports
>Synopsis:       [UPDATE]update biojava to 1.5beta2:a Java framework for processing biological data.
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Wed Mar 21 15:10:03 GMT 2007
>Closed-Date:
>Last-Modified:
>Originator:     Nemo Liu
>Release:        7-current
>Organization:
>Environment:
FreeBSD tango.sina.com.cn 7.0-STOooRM FreeBSD 7.0-STOooRM #0: Mon Mar 19 12:20:35 CST 2007     delphij at tango.sina.com.cn:/usr/obj/usr/src/sys/TANGO  amd64
>Description:
update biojava to 1.5beta2.
BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit.

BioJava is used in several real-world bioinformatics applications and has been used for bioinformatics analysis in a number of published studies. 
>How-To-Repeat:

>Fix:


Patch attached with submission follows:

? patch-biojava.diff
Index: Makefile
===================================================================
RCS file: /home/ncvs/ports/biology/biojava/Makefile,v
retrieving revision 1.12
diff -u -r1.12 Makefile
--- Makefile	11 Feb 2007 01:23:27 -0000	1.12
+++ Makefile	21 Mar 2007 14:52:25 -0000
@@ -2,12 +2,12 @@
 # Date created:	15 September 2000
 # Whom:		FreeBSD Bio porters (bio at freebsd.net)
 #
-# $FreeBSD: ports/biology/biojava/Makefile,v 1.12 2007/02/11 01:23:27 kris Exp $
+# $FreeBSD$
 #
 
 PORTNAME=	biojava
-DISTVERSION=	1.5-beta
-PORTEPOCH=	1
+DISTVERSION=	1.5-beta2
+#PORTEPOCH=	1
 CATEGORIES=	biology java
 MASTER_SITES=	http://www.biojava.org/download/bj15b/all/:source	\
 		http://www.biojava.org/download/bj15b/bin/:bin
@@ -15,7 +15,7 @@
 		bytecode.jar:bin
 EXTRACT_ONLY=	${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}
 
-MAINTAINER=	ports at FreeBSD.org
+MAINTAINER=	nemoliu at gmail.com
 COMMENT=	Open-source java tools for processing biological data
 
 BUILD_DEPENDS=	${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \
@@ -33,12 +33,8 @@
 BUILD_DEPENDS+=	${JAVALIBDIR}/junit.jar:${PORTSDIR}/java/junit
 .endif
 
-BROKEN=		Does not build
-DEPRECATED=	${BROKEN}
-EXPIRATION_DATE=2007-04-10
-
 USE_JAVA=	yes
-JAVA_VERSION=	1.4+
+JAVA_VERSION=	1.5+
 USE_ANT=	yes
 MAKE_ENV=	CLASSPATH="${JAVALIBDIR}"
 ALL_TARGET=	compile-apps
@@ -48,6 +44,7 @@
 JARFILES=	apps-${DISTVERSION}.jar biojava.jar bytecode.jar
 PORTDOCS=	biojava
 SAMPLES=	demos
+WRKSRC=${WRKDIR}
 
 .if !defined(NOPORTDOCS)
 ALL_TARGET+=	javadocs-biojava
Index: distinfo
===================================================================
RCS file: /home/ncvs/ports/biology/biojava/distinfo,v
retrieving revision 1.5
diff -u -r1.5 distinfo
--- distinfo	21 Nov 2006 22:35:28 -0000	1.5
+++ distinfo	21 Mar 2007 14:52:25 -0000
@@ -1,6 +1,6 @@
-MD5 (biojava-1.5-beta.tar.gz) = 8dc7307d9dc4bc9dd9222dfaaee5d047
-SHA256 (biojava-1.5-beta.tar.gz) = a8e0ba3a393bc70606bf7393255077b32bd1c1980f5daeec07c7362f0d2985e1
-SIZE (biojava-1.5-beta.tar.gz) = 15777707
+MD5 (biojava-1.5-beta2.tar.gz) = 904e9a5600102a9a5238b87868e3f09f
+SHA256 (biojava-1.5-beta2.tar.gz) = f2912bc90d4b9c01ac24e9db9718203af01b098538020989d4519cfabd901208
+SIZE (biojava-1.5-beta2.tar.gz) = 28767548
 MD5 (bytecode.jar) = 332e0b06b485645802067c92f1055e37
 SHA256 (bytecode.jar) = 745bf5899361565f1a3572f19d4ae9c99354856d8a9f29bf52908650c0e9e48f
 SIZE (bytecode.jar) = 93463
Index: files/patch-build.xml
===================================================================
RCS file: /home/ncvs/ports/biology/biojava/files/patch-build.xml,v
retrieving revision 1.1
diff -u -r1.1 patch-build.xml
--- files/patch-build.xml	21 Nov 2006 22:35:28 -0000	1.1
+++ files/patch-build.xml	21 Mar 2007 14:52:25 -0000
@@ -1,5 +1,5 @@
---- build.xml.orig	Thu Sep  7 11:18:13 2006
-+++ build.xml	Sun Oct 22 12:43:18 2006
+--- build.xml.orig	Fri Dec 29 14:12:28 2006
++++ build.xml	Wed Mar 21 16:14:38 2007
 @@ -49,7 +49,7 @@
  
      <property name="build.compiler" value="javac1.4" />

>Release-Note:
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