Date: Wed, 21 Mar 2007 15:00:46 GMT From: Nemo Liu<nemoliu@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/110621: [UPDATE]update biojava to 1.5beta2:a Java framework for processing biological data. Message-ID: <200703211500.l2LF0kkC040477@www.freebsd.org> Resent-Message-ID: <200703211510.l2LFA4eU020671@freefall.freebsd.org>
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>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@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@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@FreeBSD.org +MAINTAINER= nemoliu@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: >Audit-Trail: >Unformatted:
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