Attachment #76793 for bug #110621

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# Date created:	15 September 2000
# Whom:		FreeBSD Bio porters (bio@freebsd.net)
#
# $FreeBSD$
#

PORTNAME=	biojava
DISTVERSION=	1.5-beta2
PORTEPOCH=	1
CATEGORIES=	biology java
MASTER_SITES=	http://www.biojava.org/download/bj15b/all/:source	\

		bytecode.jar:bin
EXTRACT_ONLY=	${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}

MAINTAINER=	nemoliu@gmail.com
COMMENT=	Open-source java tools for processing biological data

BUILD_DEPENDS=	${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \
		${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \
		${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \
		${JAVALIBDIR}/commons-cli.jar:${PORTSDIR}/java/jakarta-commons-cli \
		${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \
		${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool \
		${JAVALIBDIR}/commons-collections.jar:${PORTSDIR}/java/jakarta-commons-collections
RUN_DEPENDS=	${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \
		${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \
		${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \

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=	1.5+
USE_ANT=	yes
MAKE_ENV=	CLASSPATH="${JAVALIBDIR}"
ALL_TARGET=	compile-apps

JARFILES=	apps-${DISTVERSION}.jar biojava.jar bytecode.jar
PORTDOCS=	biojava
SAMPLES=	demos
WRKSRC=${WRKDIR}

.if !defined(NOPORTDOCS)
ALL_TARGET+=	javadocs-biojava

Lines 1-6 Link Here

(-)distinfo (-3 / +3 lines)
1	MD5 (biojava-1.5-beta.tar.gz) = 8dc7307d9dc4bc9dd9222dfaaee5d047	1	MD5 (biojava-1.5-beta2.tar.gz) = 904e9a5600102a9a5238b87868e3f09f
2	SHA256 (biojava-1.5-beta.tar.gz) = a8e0ba3a393bc70606bf7393255077b32bd1c1980f5daeec07c7362f0d2985e1	2	SHA256 (biojava-1.5-beta2.tar.gz) = f2912bc90d4b9c01ac24e9db9718203af01b098538020989d4519cfabd901208
3	SIZE (biojava-1.5-beta.tar.gz) = 15777707	3	SIZE (biojava-1.5-beta2.tar.gz) = 28767548
4	MD5 (bytecode.jar) = 332e0b06b485645802067c92f1055e37	4	MD5 (bytecode.jar) = 332e0b06b485645802067c92f1055e37
5	SHA256 (bytecode.jar) = 745bf5899361565f1a3572f19d4ae9c99354856d8a9f29bf52908650c0e9e48f	5	SHA256 (bytecode.jar) = 745bf5899361565f1a3572f19d4ae9c99354856d8a9f29bf52908650c0e9e48f
6	SIZE (bytecode.jar) = 93463	6	SIZE (bytecode.jar) = 93463

Lines 1-5 Link Here

(-)files/patch-build.xml (-2 / +2 lines)
1	--- build.xml.orig Thu Sep 7 11:18:13 2006	1	--- build.xml.orig Fri Dec 29 14:12:28 2006
2	+++ build.xml Sun Oct 22 12:43:18 2006	2	+++ build.xml Wed Mar 21 16:14:38 2007
3	@@ -49,7 +49,7 @@	3	@@ -49,7 +49,7 @@
4		4
5	<property name="build.compiler" value="javac1.4" />	5	<property name="build.compiler" value="javac1.4" />

Return to bug 110621

Lines 2-12 Link Here

(-)Makefile (-9 / +10 lines)
2	# Date created: 15 September 2000	2	# Date created: 15 September 2000
3	# Whom: FreeBSD Bio porters (bio@freebsd.net)	3	# Whom: FreeBSD Bio porters (bio@freebsd.net)
4	#	4	#
5	# $FreeBSD: ports/biology/biojava/Makefile,v 1.12 2007/02/11 01:23:27 kris Exp $	5	# $FreeBSD$
6	#	6	#
7		7
8	PORTNAME= biojava	8	PORTNAME= biojava
9	DISTVERSION= 1.5-beta	9	DISTVERSION= 1.5-beta2
10	PORTEPOCH= 1	10	PORTEPOCH= 1
11	CATEGORIES= biology java	11	CATEGORIES= biology java
12	MASTER_SITES= http://www.biojava.org/download/bj15b/all/:source \	12	MASTER_SITES= http://www.biojava.org/download/bj15b/all/:source \
Lines 15-26 Link Here
15	bytecode.jar:bin	15	bytecode.jar:bin
16	EXTRACT_ONLY= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}	16	EXTRACT_ONLY= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}
17		17
18	MAINTAINER= ports@FreeBSD.org	18	MAINTAINER= nemoliu@gmail.com
19	COMMENT= Open-source java tools for processing biological data	19	COMMENT= Open-source java tools for processing biological data
20		20
21	BUILD_DEPENDS= ${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \	21	BUILD_DEPENDS= ${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \
		22	${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \
		23	${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \
		24	${JAVALIBDIR}/commons-cli.jar:${PORTSDIR}/java/jakarta-commons-cli \
22	${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \	25	${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \
23	${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool	26	${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool \
		27	${JAVALIBDIR}/commons-collections.jar:${PORTSDIR}/java/jakarta-commons-collections
24	RUN_DEPENDS= ${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \	28	RUN_DEPENDS= ${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \
25	${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \	29	${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \
26	${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \	30	${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \
Lines 33-44 Link Here
33	BUILD_DEPENDS+= ${JAVALIBDIR}/junit.jar:${PORTSDIR}/java/junit	37	BUILD_DEPENDS+= ${JAVALIBDIR}/junit.jar:${PORTSDIR}/java/junit
34	.endif	38	.endif
35		39
36	BROKEN= Does not build
37	DEPRECATED= ${BROKEN}
38	EXPIRATION_DATE=2007-04-10
39
40	USE_JAVA= yes	40	USE_JAVA= yes
41	JAVA_VERSION= 1.4+	41	JAVA_VERSION= 1.5+
42	USE_ANT= yes	42	USE_ANT= yes
43	MAKE_ENV= CLASSPATH="${JAVALIBDIR}"	43	MAKE_ENV= CLASSPATH="${JAVALIBDIR}"
44	ALL_TARGET= compile-apps	44	ALL_TARGET= compile-apps
Lines 48-53 Link Here
48	JARFILES= apps-${DISTVERSION}.jar biojava.jar bytecode.jar	48	JARFILES= apps-${DISTVERSION}.jar biojava.jar bytecode.jar
49	PORTDOCS= biojava	49	PORTDOCS= biojava
50	SAMPLES= demos	50	SAMPLES= demos
		51	WRKSRC=${WRKDIR}
51		52
52	.if !defined(NOPORTDOCS)	53	.if !defined(NOPORTDOCS)
53	ALL_TARGET+= javadocs-biojava	54	ALL_TARGET+= javadocs-biojava