Index: head/biology/plink/Makefile
===================================================================
--- head/biology/plink/Makefile	(revision 336327)
+++ head/biology/plink/Makefile	(revision 336328)
@@ -1,29 +1,29 @@
 # Created by: Jason Bacon <jwbacon@tds.net>
 # $FreeBSD$
 
 PORTNAME=	plink
 PORTVERSION=	1.07
 PORTREVISION=	1
 CATEGORIES=	biology science
 MASTER_SITES=	http://pngu.mgh.harvard.edu/~purcell/plink/dist/
 DISTNAME=	${PORTNAME}-${PORTVERSION}-src
 
 MAINTAINER=	jwbacon@tds.net
 COMMENT=	Whole genome association analysis toolset
 
 LICENSE=	GPLv2
 
 LIB_DEPENDS=	liblapack.so:${PORTSDIR}/math/lapack
 
+USES=		gmake
 USE_ZIP=	yes
-USE_GMAKE=	yes
 USE_FORTRAN=	yes	# Make it use the same compiler as lapack
 
 PLIST_FILES=	bin/plink
 
 NO_STAGE=	yes
 do-install:
 	${MKDIR} ${PREFIX}/bin
 	${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin
 
 .include <bsd.port.mk>
Index: head/biology/plink/files/patch-elf.cpp
===================================================================
--- head/biology/plink/files/patch-elf.cpp	(nonexistent)
+++ head/biology/plink/files/patch-elf.cpp	(revision 336328)
@@ -0,0 +1,25 @@
+--- elf.cpp.orig	2013-11-16 17:09:56.000000000 +0100
++++ elf.cpp	2013-11-16 17:10:24.000000000 +0100
+@@ -1175,10 +1175,10 @@
+ 	  << setw(8) << gcnt << " "
+ 	  << setw(8) << (double)cnt / (double)gcnt << "\n";
+ 
+-      map<int,int>::iterator i = chr_cnt.begin();
+-      while ( i != chr_cnt.end() )
++      map<int,int>::iterator ichr = chr_cnt.begin();
++      while ( ichr != chr_cnt.end() )
+ 	{
+-	  int c = i->first;
++	  int c = ichr->first;
+ 	  int x = chr_cnt.find( c )->second;
+ 	  int y = chr_gcnt.find( c )->second;
+ 	  
+@@ -1189,7 +1189,7 @@
+ 	      << setw(8) << y << " "
+ 	      << setw(8) << (double)x / (double)y << "\n";
+ 	  
+-	  ++i;
++	  ++ichr;
+ 	}
+       
+     }

Property changes on: head/biology/plink/files/patch-elf.cpp
___________________________________________________________________
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: head/biology/plink/files/patch-idhelp.cpp
===================================================================
--- head/biology/plink/files/patch-idhelp.cpp	(nonexistent)
+++ head/biology/plink/files/patch-idhelp.cpp	(revision 336328)
@@ -0,0 +1,19 @@
+--- idhelp.cpp.orig	2013-11-16 17:11:42.000000000 +0100
++++ idhelp.cpp	2013-11-16 17:12:53.000000000 +0100
+@@ -772,12 +772,12 @@
+       for (int j = 0 ; j < jointField.size(); j++ )
+ 	{
+ 	  set<IDField*> & jf = jointField[j];
+-	  set<IDField*>::iterator j = jf.begin();
++	  set<IDField*>::iterator jfit = jf.begin();
+ 	  PP->printLOG(" { ");
+-	  while ( j != jf.end() )
++	  while ( jfit != jf.end() )
+ 	    {
+-	      PP->printLOG( (*j)->name + " " );
+-	      ++j;
++	      PP->printLOG( (*jfit)->name + " " );
++	      ++jfit;
+ 	    }
+ 	  PP->printLOG(" }");
+ 	}

Property changes on: head/biology/plink/files/patch-idhelp.cpp
___________________________________________________________________
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: head/biology/plink/files/patch-sets.cpp
===================================================================
--- head/biology/plink/files/patch-sets.cpp	(nonexistent)
+++ head/biology/plink/files/patch-sets.cpp	(revision 336328)
@@ -0,0 +1,18 @@
+--- sets.cpp.orig	2013-11-16 17:06:29.000000000 +0100
++++ sets.cpp	2013-11-16 17:07:12.000000000 +0100
+@@ -768,11 +768,11 @@
+       //////////////////////////////////////////////
+       // Reset original missing status
+ 
+-      vector<Individual*>::iterator i = PP->sample.begin();
+-      while ( i != PP->sample.end() )
++      vector<Individual*>::iterator ipp = PP->sample.begin();
++      while ( ipp != PP->sample.end() )
+ 	{
+-	  (*i)->missing = (*i)->flag;
+-	  ++i;
++	  (*ipp)->missing = (*ipp)->flag;
++	  ++ipp;
+ 	}
+ 
+       ////////////////////////////////////////////////

Property changes on: head/biology/plink/files/patch-sets.cpp
___________________________________________________________________
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