Attachment 148003 Details for Bug 194163 – biology_phylip.diff

[patch] biology_phylip.diff

biology_phylip.diff (text/plain), 4.12 KB, created by tkato432 on 2014-10-05 18:30:35 UTC

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Creator: tkato432

Created: 2014-10-05 18:30:35 UTC

Size: 4.12 KB

patch

obsolete

>diff -urN /usr/ports/biology/phylip/Makefile biology/phylip/Makefile
>--- /usr/ports/biology/phylip/Makefile	2014-06-21 17:47:35.000000000 +0900
>+++ biology/phylip/Makefile	2014-10-06 00:00:00.000000000 +0900
>@@ -2,8 +2,7 @@
> # $FreeBSD: head/biology/phylip/Makefile 351411 2014-04-16 18:28:47Z zeising $
> 
> PORTNAME=	phylip
>-PORTVERSION=	3.695
>-PORTREVISION=	3
>+PORTVERSION=	3.696
> PORTEPOCH=	1
> CATEGORIES=	biology
> MASTER_SITES=	http://evolution.gs.washington.edu/phylip/download/
>@@ -11,13 +10,16 @@
> MAINTAINER=	ports@FreeBSD.org
> COMMENT=	Phylogeny Inference Package
> 
>+LICENSE=	BSD2CLAUSE
>+LICENSE_FILES=	${WRKSRC}/COPYRIGHT
>+
> BUILD_DEPENDS=	bash:${PORTSDIR}/shells/bash
> 
> BUILD_WRKSRC=	${WRKSRC}/src
> INSTALL_WRKSRC=	${WRKSRC}/src
> 
>-USE_XORG=	x11 xaw xt
> USES=		gmake
>+USE_XORG=	x11 xaw xt
> MAKEFILE=	Makefile.unx
> MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS} -DUNX" \
> 		DFLAGS="${CFLAGS} -DX -I${LOCALBASE}/include" \
>@@ -25,28 +27,23 @@
> USE_LDCONFIG=	yes
> 
> PORTDOCS=	*
>-PORTEXAMPLES=	*
>-
>-OPTIONS_DEFINE=	DOCS EXAMPLES
> 
>-pre-install:
>-	@(cd ${WRKSRC}/src && ${STRIP_CMD} libdrawtree.so libdrawgram.so)
>+OPTIONS_DEFINE=	DOCS
> 
> post-install:
> 	@cd ${WRKSRC}/exe && \
> 		${FIND} . -maxdepth 1 -not -type d -not -name '*.jar' \
> 		-not -name '*.unx' -not -name 'font*' -not -name '*.so' \
>-		-exec ${INSTALL_PROGRAM} "{}" "${STAGEDIR}${PREFIX}/bin/{}" \;
>+		| ${XARGS} -J % ${INSTALL_PROGRAM} % ${STAGEDIR}${PREFIX}/bin
> 	@cd ${WRKSRC}/exe && \
> 		${FIND} . -maxdepth 1 -not -type d -name "*.so" \
>-		-exec ${INSTALL_DATA} "{}" "${STAGEDIR}${PREFIX}/lib/{}" \;
>+		| ${XARGS} -J % ${INSTALL_LIB} % ${STAGEDIR}${PREFIX}/lib
> 	@${MKDIR} ${STAGEDIR}${DATADIR}
> 	@cd ${WRKSRC}/exe && \
> 		${FIND} . -maxdepth 1 -not -type d -name 'font*' \
>-		-exec ${INSTALL_DATA} "{}" "${STAGEDIR}${DATADIR}/{}" \;
>+		| ${XARGS} -J % ${INSTALL_DATA} % ${STAGEDIR}${DATADIR}
> 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
>-	@(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR})
>-	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
>-	@(cd ${WRKSRC}/exe && ${COPYTREE_SHARE} testdata ${STAGEDIR}${EXAMPLESDIR})
>+	@(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . \
>+		${STAGEDIR}${DOCSDIR})
> 
> .include <bsd.port.mk>
>diff -urN /usr/ports/biology/phylip/distinfo biology/phylip/distinfo
>--- /usr/ports/biology/phylip/distinfo	2014-06-21 17:47:35.000000000 +0900
>+++ biology/phylip/distinfo	2014-10-06 00:00:00.000000000 +0900
>@@ -1,2 +1,2 @@
>-SHA256 (phylip-3.695.tar.gz) = d843ecee0d6bcf57f4f23dc8ef064a668907cc69b4edd7626ff7afdd8d0de370
>-SIZE (phylip-3.695.tar.gz) = 4364684
>+SHA256 (phylip-3.696.tar.gz) = cd0a452ca51922142ad06d585e2ef98565536a227cbd2bd47a2243af72c84a06
>+SIZE (phylip-3.696.tar.gz) = 3955721
>diff -urN /usr/ports/biology/phylip/pkg-descr biology/phylip/pkg-descr
>--- /usr/ports/biology/phylip/pkg-descr	2014-06-21 17:47:35.000000000 +0900
>+++ biology/phylip/pkg-descr	2014-10-06 00:00:00.000000000 +0900
>@@ -1,17 +1,8 @@
>-              PHYLIP - Phylogeny Inference Package (version 3.6)
>-
> PHYLIP (the PHYLogeny Inference Package) is a package of programs for
>-inferring phylogenies (evolutionary trees).  Methods that are
>-available in the package include parsimony, distance matrix, and
>-likelihood methods, including bootstrapping and consensus trees. Data
>-types that can be handled include molecular sequences, gene
>-frequencies, restriction sites, distance matrices, and 0/1 discrete
>-characters.
>-
>- Joe Felsenstein
>- Department of Genetics
>- University of Washington
>- Box 357360
>- Seattle, Washington 98195-7360, U.S.A.
>+inferring phylogenies (evolutionary trees). Methods that are available
>+in the package include parsimony, distance matrix, and likelihood
>+methods, including bootstrapping and consensus trees. Data types that
>+can be handled include molecular sequences, gene frequencies,
>+restriction sites, distance matrices, and 0/1 discrete characters.
> 
> WWW: http://evolution.genetics.washington.edu/phylip.html
>diff -urN /usr/ports/biology/phylip/pkg-plist biology/phylip/pkg-plist
>--- /usr/ports/biology/phylip/pkg-plist	2014-06-21 17:47:35.000000000 +0900
>+++ biology/phylip/pkg-plist	2014-10-06 00:00:00.000000000 +0900
>@@ -41,4 +41,3 @@
> %%DATADIR%%/font4
> %%DATADIR%%/font5
> %%DATADIR%%/font6
>-@dirrm %%DATADIR%%

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Attachments on bug 194163: 148003