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1.1
date	2012.09.27.09.59.25;	author makc;	state Exp;
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1.1
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@SVN rev 304954 on 2012-09-27 09:59:25Z by makc

Add new ports biology/plink [1] and biology/plinkseq [2]:

PLINK is a free, open-source whole genome association analysis toolset.
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data.

PR:		ports/171918 [1]
PR:		ports/171922 [2]
Submitted by:	Jason Bacon <jwbacon at tds.net>
@
text
@--- Makefile.orig	2009-10-10 11:00:20.000000000 -0500
+++ Makefile	2012-09-07 08:24:26.000000000 -0500
@@@@ -26,7 +26,7 @@@@
 WITH_WEBCHECK = 1
 FORCE_32BIT = 
 WITH_ZLIB = 1
-WITH_LAPACK = 
+WITH_LAPACK = 1
 FORCE_DYNAMIC = 
 
 # Put C++ compiler here; Windows has it's own specific version
@@@@ -34,17 +34,17 @@@@
 CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
 
 # Any other compiler flags here ( -Wall, -g, etc)
-CXXFLAGS = 
+# CXXFLAGS = 
 
 # Misc
-LIB_LAPACK = /usr/lib/liblapack.so.3
+LIB_LAPACK = -L${LOCALBASE}/lib -llapack -lblas -lgfortran
 
 
 # --------------------------------------------------------------------
 # Do not edit below this line
 # --------------------------------------------------------------------
 
-CXXFLAGS += -O3 -I.
+CXXFLAGS += -I.
 OUTPUT = plink
 
 # Some system specific flags
@@@@ -58,8 +58,8 @@@@
 endif
 
 ifeq ($(SYS),UNIX)
- CXXFLAGS += -DUNIX
- CXX = $(CXX_UNIX)
+ CXXFLAGS += -DUNIX -Dfopen64=fopen
+ CXX ?= $(CXX_UNIX)
  ifndef FORCE_DYNAMIC
   CXXFLAGS += -static
  endif
@@@@ -128,7 +128,7 @@@@
 LIB += -ldl
 endif
 ifeq ($(SYS),UNIX)
-LIB += -ldl -lcrypt
+LIB += -lcrypt
 endif
 endif
 
@
