head	1.22;
access;
symbols
	RELEASE_8_3_0:1.18
	RELEASE_9_0_0:1.18
	RELEASE_7_4_0:1.18
	RELEASE_8_2_0:1.18
	RELEASE_6_EOL:1.18
	RELEASE_8_1_0:1.18
	RELEASE_7_3_0:1.18
	RELEASE_8_0_0:1.18
	RELEASE_7_2_0:1.17
	RELEASE_7_1_0:1.16
	RELEASE_6_4_0:1.16
	RELEASE_5_EOL:1.15
	RELEASE_7_0_0:1.15
	RELEASE_6_3_0:1.15
	PRE_XORG_7:1.14
	RELEASE_4_EOL:1.10
	RELEASE_6_2_0:1.8
	RELEASE_6_1_0:1.6
	RELEASE_5_5_0:1.6
	RELEASE_6_0_0:1.6
	RELEASE_5_4_0:1.6
	RELEASE_4_11_0:1.6
	RELEASE_5_3_0:1.5
	RELEASE_4_10_0:1.5
	RELEASE_5_2_1:1.5
	RELEASE_5_2_0:1.5
	RELEASE_4_9_0:1.4
	RELEASE_5_1_0:1.4
	RELEASE_4_8_0:1.4
	RELEASE_5_0_0:1.3
	RELEASE_4_7_0:1.3
	RELEASE_4_6_2:1.2
	RELEASE_4_6_1:1.2
	RELEASE_4_6_0:1.2
	RELEASE_5_0_DP1:1.2
	RELEASE_4_5_0:1.2
	RELEASE_4_4_0:1.2
	RELEASE_4_3_0:1.1
	RELEASE_4_2_0:1.1;
locks; strict;
comment	@# @;


1.22
date	2012.12.11.07.29.40;	author svnexp;	state Exp;
branches;
next	1.21;

1.21
date	2012.12.10.13.24.55;	author svnexp;	state Exp;
branches;
next	1.20;

1.20
date	2012.11.17.05.54.51;	author svnexp;	state Exp;
branches;
next	1.19;

1.19
date	2012.07.29.11.17.02;	author cs;	state Exp;
branches;
next	1.18;

1.18
date	2009.05.01.09.33.42;	author miwi;	state Exp;
branches;
next	1.17;

1.17
date	2008.12.08.06.43.45;	author linimon;	state Exp;
branches;
next	1.16;

1.16
date	2008.06.06.13.08.28;	author edwin;	state Exp;
branches;
next	1.15;

1.15
date	2007.05.19.20.00.22;	author flz;	state Exp;
branches;
next	1.14;

1.14
date	2007.04.30.06.27.37;	author nemoliu;	state Exp;
branches;
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1.13
date	2007.03.27.08.01.54;	author miwi;	state Exp;
branches;
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1.12
date	2007.02.11.01.23.27;	author kris;	state Exp;
branches;
next	1.11;

1.11
date	2007.02.05.00.08.52;	author kris;	state Exp;
branches;
next	1.10;

1.10
date	2006.12.13.12.55.58;	author linimon;	state Exp;
branches;
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1.9
date	2006.11.21.22.35.28;	author thierry;	state Exp;
branches;
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1.8
date	2006.09.02.16.50.54;	author kris;	state Exp;
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1.7
date	2006.04.22.22.09.45;	author kris;	state Exp;
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1.6
date	2004.11.22.15.47.58;	author vs;	state Exp;
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1.5
date	2003.11.02.02.48.04;	author edwin;	state Exp;
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1.4
date	2003.02.21.11.01.31;	author knu;	state Exp;
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1.3
date	2002.06.16.01.08.49;	author glewis;	state Exp;
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1.2
date	2001.07.08.18.15.31;	author ijliao;	state Exp;
branches;
next	1.1;

1.1
date	2000.10.10.11.14.03;	author jeh;	state Exp;
branches;
next	;


desc
@@


1.22
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/308665
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ## r308665 | bapt | 2012-12-11 07:26:38 +0000 (Tue, 11 Dec 2012) | 6 lines
## SVN ##
## SVN ## Remove hardcoded extract dependency on diablo-jdk16, directly use USE_ZIP
## SVN ## instead given that jar files are just zip files, remove hardcoded do extract
## SVN ## target.
## SVN ##
## SVN ## Reported by:	linimon, matthew
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ##
@
text
@# Created by: FreeBSD Bio porters (bio@@freebsd.net)
# $FreeBSD: head/biology/biojava/Makefile 308665 2012-12-11 07:26:38Z bapt $

PORTNAME=	biojava
DISTVERSION=	1.7
PORTEPOCH=	1
CATEGORIES=	biology java
MASTER_SITES=	http://www.biojava.org/download/bj17/all/
DISTNAME=	${PORTNAME}-${DISTVERSION}-all
EXTRACT_SUFX=	.jar

MAINTAINER=	wenheping@@gmail.com
COMMENT=	Open-source Java tools for processing biological data

USE_ZIP=	yes
USE_JAVA=	yes
JAVA_VERSION=	1.6+
USE_ANT=	yes
MAKE_ENV=	CLASSPATH="${JAVALIBDIR}"
ALL_TARGET=	package-biojava

JARFILES=	biojava.jar bytecode.jar
PORTDOCS=	biojava
PORTEXAMPLES=	demos
WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}

.if !defined(WITHOUT_TESTS)
regression-test:
	@@(cd ${BUILD_WRKSRC}; \
		${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests)
.endif

do-install:
	@@${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..."
	@@${MKDIR} ${JAVAJARDIR}
.for JARFILE in ${JARFILES}
	@@cd ${WRKSRC}/ant-build && ${INSTALL_DATA} ${JARFILE} ${JAVAJARDIR}/${JARFILE}
	@@${ECHO_MSG} -n " ${JARFILE}"
.endfor
	@@${ECHO_MSG} " [ DONE ]"

.if !defined(NOPORTDOCS)
	@@${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..."
	@@${MKDIR} ${DOCSDIR}
	@@${INSTALL_DATA} ${WRKSRC}/LICENSE ${DOCSDIR}
	@@${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
	@@cd ${WRKSRC}/doc && \
		${FIND} ${PORTDOCS} -type d -exec ${MKDIR} "${DOCSDIR}/{}" \; && \
		${FIND} ${PORTDOCS} -not -type d -exec ${INSTALL_DATA} "{}" "${DOCSDIR}/{}" \;
	@@${ECHO_MSG} " [ DONE ]"
.endif

.if !defined(NOPORTEXAMPLES)
	@@${ECHO_MSG} -n ">> Installing examples in ${EXAMPLESDIR}..."
	@@${MKDIR} ${EXAMPLESDIR}
	cd ${WRKSRC}/doc && \
		${FIND} ${PORTEXAMPLES} -type d -exec ${MKDIR} "${EXAMPLESDIR}/{}" \; && \
		${FIND} ${PORTEXAMPLES} -not -type d -exec ${INSTALL_DATA} "{}" "${EXAMPLESDIR}/{}" \;
	@@${ECHO_MSG} " [ DONE ]"
.endif

post-install:
.if !defined(BATCH)
	@@${ECHO_MSG} ""
	@@${ECHO_MSG} "Libraries installed at: ${JAVAJARDIR}"
	@@${ECHO_MSG} "You should edit your CLASSPATH to include the jar files"
	@@${ECHO_MSG} "in this directory."
	@@${ECHO_MSG} ""
	@@${ECHO_MSG} "Docs and demos are installed in:"
	@@${ECHO_MSG} "${DOCSDIR}"
	@@${ECHO_MSG} ""
.endif

.include <bsd.port.mk>
@


1.21
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/308604
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ## r308604 | bapt | 2012-12-10 13:18:28 +0000 (Mon, 10 Dec 2012) | 3 lines
## SVN ##
## SVN ## Decommissioning java 1.5 (EOLed since October 2009):
## SVN ## suppress any reference to JAVA_VERSION=	1.5+ (part2)
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ##
@
text
@d2 1
a2 1
# $FreeBSD: head/biology/biojava/Makefile 308604 2012-12-10 13:18:28Z bapt $
d15 1
a15 2
EXTRACT_DEPENDS+=	jar:${PORTSDIR}/java/diablo-jdk16

a24 1
EXTRACT_CMD=	jar -xvf ${_DISTDIR}/${DISTFILES}
a26 5
do-extract:
	@@${RM} -rf ${WRKDIR}
	@@${MKDIR} ${WRKDIR}
	@@cd ${WRKDIR} && ${EXTRACT_CMD}

@


1.20
log
@Switch exporter over
@
text
@d1 2
a2 6
# New ports collection makefile for: biojava
# Date created:	15 September 2000
# Whom:		FreeBSD Bio porters (bio@@freebsd.net)
#
# $FreeBSD: head/biology/biojava/Makefile 301684 2012-07-29 11:17:02Z cs $
#
d18 1
a18 1
JAVA_VERSION=	1.5+
@


1.19
log
@SVN rev 301684 on 2012-07-29 11:17:02Z by cs

Fix typos in COMMENT

Approved by:	portmgr@@ (implicit)
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.18
log
@- Update to 1.7
- Pass maintainership to submitter

PR:		134056
Submitted by:	Wen Heping <wenheping@@gmail.com>
@
text
@d17 1
a17 1
COMMENT=	Open-source java tools for processing biological data
@


1.17
log
@Reset nemoliu due to maintainer-timeouts and no response to email.

Hat:	portmgr
@
text
@d9 1
a9 2
DISTVERSION=	1.5-beta2
PORTREVISION=	2
d12 3
a14 5
MASTER_SITES=	http://www.biojava.org/download/bj15b/all/:source	\
		http://www.biojava.org/download/bj15b/bin/:bin
DISTFILES=	${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}:source	\
		bytecode.jar:bin
EXTRACT_ONLY=	${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}
d16 1
a16 1
MAINTAINER=	ports@@FreeBSD.org
d19 1
a19 18
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 \
		${JAVALIBDIR}/commons-cli.jar:${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

.if !defined(WITHOUT_TESTS)
BUILD_DEPENDS+=	${JAVALIBDIR}/junit.jar:${PORTSDIR}/java/junit
.endif
d25 1
a25 1
ALL_TARGET=	compile-apps
d27 1
a27 3
PLIST_SUB+=	VER=${DISTVERSION}

JARFILES=	apps-${DISTVERSION}.jar biojava.jar bytecode.jar
d29 8
a36 15
SAMPLES=	demos
WRKSRC=${WRKDIR}

.if !defined(NOPORTDOCS)
ALL_TARGET+=	javadocs-biojava
.endif
.if !defined(WITHOUT_SAMPLES)
ALL_TARGET+=	compile-demos
PLIST_SUB+=	INSTEX=""
.else
PLIST_SUB+=	INSTEX="@@comment "
.endif

post-extract:
	${CP} ${_DISTDIR}/bytecode.jar ${WRKSRC}
a43 1
# from textproc/xerces-j
d52 1
d58 1
a58 1
	@@cd ${WRKSRC}/ant-build/docs && \
d63 7
a69 5
.if !defined(WITHOUT_SAMPLES)
	@@${ECHO_MSG} -n ">> Installing demos in ${EXAMPLESDIR}..."
	cd ${WRKSRC} && \
		${FIND} ${SAMPLES} -type d -exec ${MKDIR} "${EXAMPLESDIR}/{}" \; && \
		${FIND} ${SAMPLES} -not -type d -exec ${INSTALL_DATA} "{}" "${EXAMPLESDIR}/{}" \;
@


1.16
log
@Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@@
Approved by:    portmgr (pav)
@
text
@d19 1
a19 1
MAINTAINER=	nemoliu@@FreeBSD.org
@


1.15
log
@- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
@
text
@d10 1
a10 1
PORTREVISION=	1
@


1.14
log
@Use my @@FreeBSD.org address.

Approved by:	delphij (mentor)
@
text
@d10 1
@


1.13
log
@- Update to 1.5-beta2
- Pass maintainership to submitter

PR:             110621
Submitted by:   Nemo Liu<nemoliu@@gmail.com>
@
text
@d18 1
a18 1
MAINTAINER=	nemoliu@@gmail.com
@


1.12
log
@Schedule these broken ports for removal on 2007-04-10 if they are still
broken at that time and no fix has been submitted.
@
text
@d9 1
a9 1
DISTVERSION=	1.5-beta
d18 1
a18 1
MAINTAINER=	ports@@FreeBSD.org
d22 3
d26 2
a27 1
		${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool
a39 4
BROKEN=		Does not build
DEPRECATED=	${BROKEN}
EXPIRATION_DATE=2007-04-10

d41 1
a41 1
JAVA_VERSION=	1.4+
d51 1
@


1.11
log
@BROKEN: Does not build
@
text
@d37 2
@


1.10
log
@Reset whitekid@@gmail.com after timeouts and no response to email.

Hat:		portmgr
@
text
@d36 2
@


1.9
log
@- Upgrade to the latest beta and unbreak;

- Add a regression-test target;

- Fix plist for WITHOUT_SAMPLES.

PR:		ports/104685
Approved by:	maintainer's time-out (1 month)
@
text
@d18 1
a18 1
MAINTAINER=	whitekid@@gmail.com
@


1.8
log
@Schedule these broken ports for termination on 2006-12-01
@
text
@d9 2
a10 1
PORTVERSION=	1.30
d12 5
a16 1
MASTER_SITES=	http://www.biojava.org/download/source/
d21 10
a30 2
RUN_DEPENDS=	${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \
		${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp
d32 3
a34 3
BROKEN=		Does not compile
DEPRECATED=	${BROKEN}
EXPIRATION_DATE=2006-12-01
d37 1
a37 1
JAVA_VERSION=	1.3+
d39 4
d44 3
a46 3
JARFILES=	biojava.jar bytecode.jar
PORTDOCS=	api
SAMPLES=	demos demos-1.4 demos-obsolete
a47 1
post-build:
d49 16
a64 2
	@@${ECHO_MSG} -n ">> Build javadocs..."
	@@cd ${WRKSRC} && ant javadocs
a85 1

@


1.7
log
@BROKEN: Does not compile
@
text
@d20 2
@


1.6
log
@- Update biology/biojava to 1.30
- Install javadoc and example files
- Assign maintainership to submitter

PR:		ports/73391
Submitted by:	Cheng-Dae Choe
Add. reviewing:	hq@@
@
text
@d19 2
@


1.5
log
@ports with possibly unreachable MAINTAINERs
*** addresses that seem to be dead:

PR:		ports/58694
Submitted by:	Oliver Eikemeier <eikemeier@@fillmore-labs.com>
@
text
@d9 1
a9 1
PORTVERSION=	1.01
d13 1
a13 1
MAINTAINER=	ports@@FreeBSD.org
d16 2
a17 1
BUILD_DEPENDS=	${JAVA_COMMAND}:${PORTSDIR}/java/linux-sun-jdk12
d19 7
a25 11
JDK_VERSION=	1.2.2
JAVAVERSION=	linux-sun-jdk${JDK_VERSION}
JAVADIR=	${PREFIX}/${JAVAVERSION}
JAVA_COMPILE=	${JAVADIR}/bin/javac
JAVA_COMMAND=	${JAVADIR}/bin/java

do-build:
	@@(cd ${WRKSRC}; \
		${JAVA_COMPILE} build/Builder.java; \
		${SETENV} PATH=${PATH}:${JAVADIR}/bin \
		${JAVA_COMMAND} build.Builder all;)
d27 1
d29 2
a30 2
	@@(cd ${WRKSRC}; ${SETENV} PATH=${PATH}:${JAVADIR}/bin \
	${JAVA_COMMAND} build.Builder docs;)
d33 1
d35 17
a51 7
	@@(cd ${WRKSRC}; \
		${MKDIR} ${PREFIX}/share/java/classes/; \
		${CP} ${WRKSRC}/biojava.jar ${PREFIX}/share/java/classes/; \
		${CP} ${WRKSRC}/xml.jar ${PREFIX}/share/java/classes/; \
		${MKDIR} ${PREFIX}/share/java/${PKGNAME}/; \
		${CP} -R README LICENSE ${PREFIX}/share/java/${PKGNAME}/; \
		${CP} -R ${WRKSRC}/demos ${PREFIX}/share/java/${PKGNAME}/;)
d53 7
a59 3
.if !defined(NOPORTDOCS)
	@@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/doc/${PKGNAME})
.endif)
d64 1
a64 1
	@@${ECHO_MSG} "Libraries installed at: ${PREFIX}/share/java/classes/"
d69 1
a69 1
	@@${ECHO_MSG} "${PREFIX}/share/java/${PKGNAME}"
@


1.4
log
@De-pkg-comment.
@
text
@d13 1
a13 1
MAINTAINER=	bio@@freebsd.net
@


1.3
log
@Unbreak this port:

. Fix dependencies to be in sync with the recent JDK ports renaming.
. Replace MASTER_SITES with a location that actually contains the
  source.
. Fix the packing list.

Note that there is a much newer version of this application available,
but that is beyond the scope of what I was trying to do (just fix the
JDK dependency), as is the last two items.
@
text
@d14 1
@


1.2
log
@Add NOPORTDOCS support to pkg-plist
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/biojava/Makefile,v 1.1 2000/10/10 11:14:03 jeh Exp $
d11 1
a11 1
MASTER_SITES=	ftp://ftp.biojava.org/pub/biojava/source/
d15 1
a15 1
BUILD_DEPENDS=	${JAVA_COMMAND}:${PORTSDIR}/java/linux-jdk
d18 1
a18 1
JAVAVERSION=	linux-jdk${JDK_VERSION}
@


1.1
log
@Initial import of biology/biojava

PR:		21678
Submitted by:	Brad Chapman <chapmanb@@arches.uga.edu>
@
text
@d5 1
a5 1
# $FreeBSD$
d44 1
a44 1
	@@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/java/${PKGNAME})
@

