Attachment #211736 for bug #243733

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# $FreeBSD$

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>

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(-)biology/plink/distinfo (+3 lines)
	1	TIMESTAMP = 1582006725
	2	SHA256 (chrchang-plink-ng-v1.90b6.16-a2002c8_GH0.tar.gz) = 34524ae326d4f547cc49961a2ca66ca2d80d1c34eb8d9d977ec9a78005d20643
	3	SIZE (chrchang-plink-ng-v1.90b6.16-a2002c8_GH0.tar.gz) = 2985789




--- 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

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(-)biology/plink/pkg-descr (+9 lines)
	1	PLINK is a widely used toolset for genome-wide association studies (GWAS) and
	2	research in population genetics.
	3
	4	Citation:
	5	Chang et al. (2015)
	6	Second-generation PLINK: rising to the challenge of larger and richer datasets.
	7	GigaScience 4(1) doi:10.1186/s13742-015-0047-8
	8
	9	WWW: https://www.cog-genomics.org/plink/

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(-)biology/plink/pkg-plist (+4 lines)
	1	bin/plink
	2	bin/prettify
	3	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.map
	4	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.ped

Return to bug 243733

Line 0 Link Here

(-)biology/plink/Makefile (+57 lines)
	1	# $FreeBSD$
	2
	3	PORTNAME= plink
	4	DISTVERSIONPREFIX= v
	5	DISTVERSION= 1.90b6.16
	6	CATEGORIES= biology
	7
	8	MAINTAINER= mzaki@e-mail.ne.jp
	9	COMMENT= Whole genome association analysis toolset
	10
	11	LICENSE= GPLv3
	12	LICENSE_FILE= ${WRKSRC}/LICENSE
	13
	14	NOT_FOR_ARCHS= aarch64 mips64 powerpc64 sparc64
	15	NOT_FOR_ARCHS_REASON= 64bit code requires SSE2 instructions
	16
	17	USES= gmake fortran
	18
	19	USE_GITHUB= yes
	20	GH_ACCOUNT= chrchang
	21	GH_PROJECT= plink-ng
	22	GH_TAGNAME= a2002c8
	23
	24	WRKSRC_SUBDIR= 1.9
	25	MAKEFILE= Makefile.std
	26	MAKE_ARGS= ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}"
	27	CFLAGS+= -DDYNAMIC_ZLIB -I${LOCALBASE}/include
	28	LDFLAGS+= -lthr
	29	INSTALL_TARGET= install-strip
	30
	31	OPTIONS_DEFINE= EXAMPLES
	32	OPTIONS_SINGLE= BLAS
	33	OPTIONS_SINGLE_BLAS= NETLIB OPENBLAS
	34	OPTIONS_DEFAULT= OPENBLAS
	35
	36	BLAS_DESC= BLAS/LAPACK implementation
	37
	38	OPENBLAS_USES= blaslapack:openblas
	39
	40	NETLIB_DESC= Netlib's reference
	41	NETLIB_USES= blaslapack:netlib
	42	NETLIB_LIB_DEPENDS= libcblas.so:math/cblas
	43	NETLIB_LDFLAGS= -lcblas
	44
	45	EXAMPLES= toy.map toy.ped
	46
	47	post-build:
	48	(cd ${WRKSRC}; ${CC} ${CFLAGS} prettify.c -o prettify)
	49
	50	post-install:
	51	${INSTALL_PROGRAM} ${WRKSRC}/prettify ${STAGEDIR}${PREFIX}/bin
	52
	53	post-install-EXAMPLES-on:
	54	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
	55	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR}
	56
	57	.include <bsd.port.mk>

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(-)biology/plink/files/patch-plink__common.h (+20 lines)
	1	--- plink_common.h.orig 2020-01-22 01:51:56 UTC
	2	+++ plink_common.h
	3	@@ -122,7 +122,7 @@
	4	#define EOLN_STR "\n"
	5	#define FOPEN_RB "r"
	6	#define FOPEN_WB "w"
	7	- #ifndef __APPLE__
	8	+ #if !defined(__APPLE__) && !defined(__FreeBSD__)
	9	// argh
	10	// not sure what the right threshold actually is, but this works for now
	11	// (may break on gcc <3.0? but that shouldn't matter anymore)
	12	@@ -143,7 +143,7 @@
	13	#define CLZLU __builtin_clzl
	14	#ifndef __LP64__
	15	// attempt to patch GCC 6 build failure
	16	- #if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
	17	+ #if !defined(__FreeBSD__) && (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
	18	#ifndef uintptr_t
	19	#define uintptr_t unsigned long
	20	#endif