FreeBSD Bugzilla – Attachment 76793 Details for
Bug 110621
[UPDATE]update biojava to 1.5beta2:a Java framework for processing biological data.
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[patch]
patch-biojava.txt
patch-biojava.txt (text/plain), 3.54 KB, created by
Nemo Liu
on 2007-03-23 15:28:13 UTC
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Description:
patch-biojava.txt
Filename:
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Creator:
Nemo Liu
Created:
2007-03-23 15:28:13 UTC
Size:
3.54 KB
patch
obsolete
>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 23 Mar 2007 15:26:12 -0000 >@@ -2,11 +2,11 @@ > # 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 >+DISTVERSION= 1.5-beta2 > PORTEPOCH= 1 > CATEGORIES= biology java > MASTER_SITES= http://www.biojava.org/download/bj15b/all/:source \ >@@ -15,12 +15,16 @@ > 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 \ >+ ${JAVALIBDIR}/xml-apis.jar:${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 >+ ${JAVALIBDIR}/commons-pool.jar:${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 \ >@@ -33,12 +37,8 @@ > 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 +48,7 @@ > 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 23 Mar 2007 15:26:12 -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 23 Mar 2007 15:26:12 -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" />
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bug 110621
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