Attachment 211736 Details for Bug 243733 – svn diff for biology/plink version 1.90.b6.16

[patch] svn diff for biology/plink version 1.90.b6.16

plink.diff (text/plain), 5.36 KB, created by Motomichi Matsuzaki on 2020-02-18 07:08:59 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Motomichi Matsuzaki

Created: 2020-02-18 07:08:59 UTC

Size: 5.36 KB

patch

obsolete

>Index: biology/plink/Makefile
>===================================================================
>--- biology/plink/Makefile	(nonexistent)
>+++ biology/plink/Makefile	(working copy)
>@@ -0,0 +1,57 @@
>+# $FreeBSD$
>+
>+PORTNAME=	plink
>+DISTVERSIONPREFIX=	v
>+DISTVERSION=	1.90b6.16
>+CATEGORIES=	biology
>+
>+MAINTAINER=	mzaki@e-mail.ne.jp
>+COMMENT=	Whole genome association analysis toolset
>+
>+LICENSE=	GPLv3
>+LICENSE_FILE=	${WRKSRC}/LICENSE
>+
>+NOT_FOR_ARCHS=	aarch64 mips64 powerpc64 sparc64
>+NOT_FOR_ARCHS_REASON=	64bit code requires SSE2 instructions
>+
>+USES=		gmake fortran
>+
>+USE_GITHUB=	yes
>+GH_ACCOUNT=	chrchang
>+GH_PROJECT=	plink-ng
>+GH_TAGNAME=	a2002c8
>+
>+WRKSRC_SUBDIR=	1.9
>+MAKEFILE=	Makefile.std
>+MAKE_ARGS=	ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}"
>+CFLAGS+=	-DDYNAMIC_ZLIB -I${LOCALBASE}/include
>+LDFLAGS+=	-lthr
>+INSTALL_TARGET=	install-strip
>+
>+OPTIONS_DEFINE=		EXAMPLES
>+OPTIONS_SINGLE=		BLAS
>+OPTIONS_SINGLE_BLAS=	NETLIB OPENBLAS
>+OPTIONS_DEFAULT=	OPENBLAS
>+
>+BLAS_DESC=	BLAS/LAPACK implementation
>+
>+OPENBLAS_USES=	blaslapack:openblas
>+
>+NETLIB_DESC=	Netlib's reference
>+NETLIB_USES=	blaslapack:netlib
>+NETLIB_LIB_DEPENDS=	libcblas.so:math/cblas
>+NETLIB_LDFLAGS=	-lcblas
>+
>+EXAMPLES=	toy.map toy.ped
>+
>+post-build:
>+	(cd ${WRKSRC}; ${CC} ${CFLAGS} prettify.c -o prettify)
>+
>+post-install:
>+	${INSTALL_PROGRAM} ${WRKSRC}/prettify ${STAGEDIR}${PREFIX}/bin
>+
>+post-install-EXAMPLES-on:
>+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
>+	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR}
>+
>+.include <bsd.port.mk>
>
>Property changes on: biology/plink/Makefile
>___________________________________________________________________
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:keywords
>## -0,0 +1 ##
>+FreeBSD=%H
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: biology/plink/distinfo
>===================================================================
>--- biology/plink/distinfo	(nonexistent)
>+++ biology/plink/distinfo	(working copy)
>@@ -0,0 +1,3 @@
>+TIMESTAMP = 1582006725
>+SHA256 (chrchang-plink-ng-v1.90b6.16-a2002c8_GH0.tar.gz) = 34524ae326d4f547cc49961a2ca66ca2d80d1c34eb8d9d977ec9a78005d20643
>+SIZE (chrchang-plink-ng-v1.90b6.16-a2002c8_GH0.tar.gz) = 2985789
>
>Property changes on: biology/plink/distinfo
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: biology/plink/files/patch-plink__common.h
>===================================================================
>--- biology/plink/files/patch-plink__common.h	(nonexistent)
>+++ biology/plink/files/patch-plink__common.h	(working copy)
>@@ -0,0 +1,20 @@
>+--- plink_common.h.orig	2020-01-22 01:51:56 UTC
>++++ plink_common.h
>+@@ -122,7 +122,7 @@
>+   #define EOLN_STR "\n"
>+   #define FOPEN_RB "r"
>+   #define FOPEN_WB "w"
>+-  #ifndef __APPLE__
>++  #if !defined(__APPLE__) && !defined(__FreeBSD__)
>+     // argh
>+     // not sure what the right threshold actually is, but this works for now
>+     // (may break on gcc <3.0?  but that shouldn't matter anymore)
>+@@ -143,7 +143,7 @@
>+   #define CLZLU __builtin_clzl
>+   #ifndef __LP64__
>+     // attempt to patch GCC 6 build failure
>+-    #if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
>++    #if !defined(__FreeBSD__) && (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
>+       #ifndef uintptr_t
>+         #define uintptr_t unsigned long
>+       #endif
>
>Property changes on: biology/plink/files/patch-plink__common.h
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: biology/plink/pkg-descr
>===================================================================
>--- biology/plink/pkg-descr	(nonexistent)
>+++ biology/plink/pkg-descr	(working copy)
>@@ -0,0 +1,9 @@
>+PLINK is a widely used toolset for genome-wide association studies (GWAS) and
>+research in population genetics.
>+
>+Citation:
>+Chang et al. (2015)
>+Second-generation PLINK: rising to the challenge of larger and richer datasets.
>+GigaScience 4(1) doi:10.1186/s13742-015-0047-8
>+
>+WWW: https://www.cog-genomics.org/plink/
>
>Property changes on: biology/plink/pkg-descr
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: biology/plink/pkg-plist
>===================================================================
>--- biology/plink/pkg-plist	(nonexistent)
>+++ biology/plink/pkg-plist	(working copy)
>@@ -0,0 +1,4 @@
>+bin/plink
>+bin/prettify
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.map
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.ped
>
>Property changes on: biology/plink/pkg-plist
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

Actions: View | Diff

Attachments on bug 243733: 211196 | 211736