Attachment 132291 Details for Bug 176552 – file.diff

[patch] file.diff

file.diff (text/plain), 6.89 KB, created by tkato432 on 2013-02-28 18:10:08 UTC

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Creator: tkato432

Created: 2013-02-28 18:10:08 UTC

Size: 6.89 KB

patch

obsolete

>diff -urN /usr/ports/biology/wise/Makefile biology/wise/Makefile
>--- /usr/ports/biology/wise/Makefile	2012-11-08 06:54:19.000000000 +0900
>+++ biology/wise/Makefile	2013-02-19 03:24:19.000000000 +0900
>@@ -1,24 +1,30 @@
>-# New ports collection makefile for:	wise
>-# Date created:				26 February 2002
>-# Whom:					Tony Maher <tonym@biolateral.com.au>
>-#
>+# Created by: Tony Maher <tonym@biolateral.com.au>
> # $FreeBSD: head/biology/wise/Makefile 300895 2012-07-14 12:56:14Z beat $
>-#
> 
> PORTNAME=	wise
>-PORTVERSION=	2.2.0
>+PORTVERSION=	2.4.1
> CATEGORIES=	biology
>-MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
>+MASTER_SITES=	http://www.ebi.ac.uk/~birney/wise2/
> DISTNAME=	${PORTNAME}${PORTVERSION}
> 
> MAINTAINER=	ports@FreeBSD.org
> COMMENT=	Intelligent algorithms for DNA searches
> 
>-WRKTOP=		${WRKDIR}/${DISTNAME}
>-WRKSRC=		${WRKTOP}/src
>+OPTIONS_DEFINE=	DOCS EXAMPLES
>+
>+BUILD_WRKSRC=	${WRKSRC}/src
>+
>+USE_GNOME=	glib20
> MAKEFILE=	makefile
>+MAKE_JOBS_SAFE=	yes
>+
> SUB_FILES=	pkg-message
> 
>+PORTDOCS=	*
>+PORTEXAMPLES=	*
>+PLIST_FILES=	${BINFILES:S,^,bin/,} ${DATAFILES:S,^,%%DATADIR%%/,}
>+PLIST_DIRS=	%%DATADIR%%
>+
> #
> # Actually want an 'ALL_TARGET = all perl' which then requires
> # 'USE_PERL5= yes' but the perl sub-build is currently broken.
>@@ -29,68 +35,44 @@
> # something like '@cd ${WRKSRC}/perl/Wise2; ${MAKE} install'
> #
> 
>-BINFILES=	dba dnal estwise estwisedb genewise genewisedb \
>-		genomewise psw pswdb
>-DATAFILES=	BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla \
>-		aa.rnd blosum30.bla blosum62.bla cb.tmf codon.table \
>-		gene.stat gon120.bla gon160.bla gon200.bla gon250.bla \
>-		gon350.bla human.gf human.gp human.stats idenity.bla \
>-		methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf
>-DOCFILES=	README apiend.tex appendix.tex dynamite.tex \
>-		genewise21.eps genewise6.eps gettex.pl makefile \
>-		wise2.tex wise2api.tex wise3arch.tex
>-EXFILES=	README db.hmm hn_est.fa human.genomic \
>-		keratin_intron.human keratin_intron.mouse pep.fa \
>-		road.pep rrm.HMM vav.dna xeno.cdna xeno.pep
>-
>-#
>-# Top level makefile does not respect CFLAGS.  Fixing it means
>-# having to fix some of the sub-directory makefiles.
>-# Note: some makefiles are ok and know that '-c' does not belong
>-# in CFLAGS and are part of the rule.
>-#
>-
>-post-configure:
>-	@${REINPLACE_CMD} \
>-		-e s'#^CFLAGS = -c -O#CFLAGS ?= -c -O#;' \
>-		-e s'#\tcsh welcome.csh##;' \
>-		${WRKSRC}/${MAKEFILE}
>-	@${REINPLACE_CMD} \
>-		-e s'#CFLAGS) $?#CFLAGS) -c $?#;' \
>-		${WRKSRC}/base/${MAKEFILE}
>-	@${REINPLACE_CMD} \
>-		-e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \
>-		${WRKSRC}/dynlibsrc/${MAKEFILE}
>-	@${REINPLACE_CMD} \
>-		-e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \
>-		-e s'#CFLAGS) estwise.c#CFLAGS) -c estwise.c#;' \
>-		-e s'#CFLAGS) estwiseb.c#CFLAGS) -c estwiseb.c#;' \
>-		-e s'#CFLAGS) estwisedb.c#CFLAGS) -c estwisedb.c#;' \
>-		-e s'#CFLAGS) genewise.c#CFLAGS) -c genewise.c#;' \
>-		-e s'#CFLAGS) genewisedb.c#CFLAGS) -c genewisedb.c#;' \
>-		${WRKSRC}/models/${MAKEFILE}
>+BINFILES=	dba dnal estwise estwisedb genewise genewisedb promoterwise \
>+		psw pswdb scanwise scanwise_server
>+DATAFILES=	BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd \
>+		cb.tmf codon.table gene.stat gon120.bla gon160.bla \
>+		gon200.bla gon250.bla gon350.bla human.gf human.gp \
>+		human.stats idenity.bla methods pb.gf pombe.gf tm.pri \
>+		wise.2 wise.per worm.gf
>+
>+.include <bsd.port.options.mk>
>+
>+post-patch:
>+	@${FIND} ${BUILD_WRKSRC} -name "makefile" | ${XARGS} \
>+		${REINPLACE_CMD} -e \
>+		's|^CC =|CC ?=| ; \
>+		 s|^CFLAGS =|CFLAGS +=| ; \
>+		 s|-O[0-9] | | ; \
>+		 s|-g | | ; \
>+		 s|-g[0-9] | | ; \
>+		 s|-lpthread|-pthread| ; \
>+		 s|glib-config|pkg-config glib-2.0| ; \
>+		 /welcome.csh/s|^|#|'
> 
> do-install:
>-.for file in ${BINFILES}
>-	@${INSTALL_PROGRAM} ${WRKSRC}/bin/${file} ${PREFIX}/bin
>+.for i in ${BINFILES}
>+	(cd ${BUILD_WRKSRC}/bin && ${INSTALL_PROGRAM} ${i} ${PREFIX}/bin)
> .endfor
> 	@${MKDIR} ${DATADIR}
>-.for file in ${DATAFILES}
>-	@${INSTALL_DATA} ${WRKTOP}/wisecfg/${file} ${DATADIR}
>+.for i in ${DATAFILES}
>+	(cd ${WRKSRC}/wisecfg && ${INSTALL_DATA} ${i} ${DATADIR})
> .endfor
>-.if !defined(NOPORTDOCS)
>+.if ${PORT_OPTIONS:MDOCS}
> 	@${MKDIR} ${DOCSDIR}
>-.for file in ${DOCFILES}
>-	@${INSTALL_DATA} ${WRKTOP}/docs/${file} ${DOCSDIR}
>-.endfor
>+	@(cd ${WRKSRC}/docs && ${COPYTREE_SHARE} . ${DOCSDIR})
>+.endif
>+.if ${PORT_OPTIONS:MEXAMPLES}
> 	 @${MKDIR} ${EXAMPLESDIR}
>-.for file in ${EXFILES}
>-	@${INSTALL_DATA} ${WRKTOP}/test_data/${file} ${EXAMPLESDIR}
>-.endfor
>-
>+	@(cd ${WRKSRC}/test_data && ${COPYTREE_SHARE} . ${EXAMPLESDIR})
> .endif
>-
>-post-install:
> 	@${CAT} ${PKGMESSAGE}
> 
> .include <bsd.port.mk>
>diff -urN /usr/ports/biology/wise/distinfo biology/wise/distinfo
>--- /usr/ports/biology/wise/distinfo	2012-11-08 06:54:19.000000000 +0900
>+++ biology/wise/distinfo	2013-02-19 02:23:09.000000000 +0900
>@@ -1,2 +1,2 @@
>-SHA256 (wise2.2.0.tar.gz) = 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780
>-SIZE (wise2.2.0.tar.gz) = 2108151
>+SHA256 (wise2.4.1.tar.gz) = 240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1
>+SIZE (wise2.4.1.tar.gz) = 3193910
>diff -urN /usr/ports/biology/wise/pkg-plist biology/wise/pkg-plist
>--- /usr/ports/biology/wise/pkg-plist	2012-11-08 06:54:19.000000000 +0900
>+++ biology/wise/pkg-plist	1970-01-01 09:00:00.000000000 +0900
>@@ -1,61 +0,0 @@
>-bin/genomewise
>-%%PORTDOCS%%%%DOCSDIR%%/README
>-%%PORTDOCS%%%%DOCSDIR%%/apiend.tex
>-%%PORTDOCS%%%%DOCSDIR%%/appendix.tex
>-%%PORTDOCS%%%%DOCSDIR%%/dynamite.tex
>-%%PORTDOCS%%%%DOCSDIR%%/genewise21.eps
>-%%PORTDOCS%%%%DOCSDIR%%/genewise6.eps
>-%%PORTDOCS%%%%DOCSDIR%%/gettex.pl
>-%%PORTDOCS%%%%DOCSDIR%%/makefile
>-%%PORTDOCS%%%%DOCSDIR%%/wise2.tex
>-%%PORTDOCS%%%%DOCSDIR%%/wise2api.tex
>-%%PORTDOCS%%%%DOCSDIR%%/wise3arch.tex
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db.hmm
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hn_est.fa
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/human.genomic
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/keratin_intron.human
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/keratin_intron.mouse
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pep.fa
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/road.pep
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rrm.HMM
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vav.dna
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xeno.cdna
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xeno.pep
>-%%DATADIR%%/BLOSUM30.bla
>-%%DATADIR%%/BLOSUM45.bla
>-%%DATADIR%%/BLOSUM62.bla
>-%%DATADIR%%/BLOSUM80.bla
>-%%DATADIR%%/aa.rnd
>-%%DATADIR%%/blosum30.bla
>-%%DATADIR%%/blosum62.bla
>-%%DATADIR%%/cb.tmf
>-%%DATADIR%%/codon.table
>-%%DATADIR%%/gene.stat
>-%%DATADIR%%/gon120.bla
>-%%DATADIR%%/gon160.bla
>-%%DATADIR%%/gon200.bla
>-%%DATADIR%%/gon250.bla
>-%%DATADIR%%/gon350.bla
>-%%DATADIR%%/human.gf
>-%%DATADIR%%/human.gp
>-%%DATADIR%%/human.stats
>-%%DATADIR%%/idenity.bla
>-%%DATADIR%%/methods
>-%%DATADIR%%/pb.gf
>-%%DATADIR%%/pombe.gf
>-%%DATADIR%%/tm.pri
>-%%DATADIR%%/wise.2
>-%%DATADIR%%/wise.per
>-%%DATADIR%%/worm.gf
>-bin/dba
>-bin/dnal
>-bin/estwise
>-bin/estwisedb
>-bin/genewise
>-bin/genewisedb
>-bin/psw
>-bin/pswdb
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%
>-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
>-@dirrm %%DATADIR%%

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Attachments on bug 176552: 132291