3 files changed, 68 insertions, 0 deletions
diff --git a/biology/plink/patches/patch-elf.cpp b/biology/plink/patches/patch-elf.cpp
new file mode 100644
index 00000000000..27f3633e690
--- /dev/null
+++ b/biology/plink/patches/patch-elf.cpp
@@ -0,0 +1,27 @@
+$NetBSD: patch-elf.cpp,v 1.1 2012/11/16 00:32:07 joerg Exp $
+
+--- elf.cpp.orig	2012-11-15 12:41:01.000000000 +0000
++++ elf.cpp
+@@ -1175,10 +1175,10 @@ void Plink::elfBaseline()
+ 	  << 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 i2 = chr_cnt.begin();
++      while ( i2 != chr_cnt.end() )
+ 	{
+-	  int c = i->first;
++	  int c = i2->first;
+ 	  int x = chr_cnt.find( c )->second;
+ 	  int y = chr_gcnt.find( c )->second;
+ 	  
+@@ -1189,7 +1189,7 @@ void Plink::elfBaseline()
+ 	      << setw(8) << y << " "
+ 	      << setw(8) << (double)x / (double)y << "\n";
+ 	  
+-	  ++i;
++	  ++i2;
+ 	}
+       
+     }
diff --git a/biology/plink/patches/patch-idhelp.cpp b/biology/plink/patches/patch-idhelp.cpp
new file mode 100644
index 00000000000..866bbc0b897
--- /dev/null
+++ b/biology/plink/patches/patch-idhelp.cpp
@@ -0,0 +1,21 @@
+$NetBSD: patch-idhelp.cpp,v 1.1 2012/11/16 00:32:07 joerg Exp $
+
+--- idhelp.cpp.orig	2012-11-15 12:44:01.000000000 +0000
++++ idhelp.cpp
+@@ -772,12 +772,12 @@ void IDHelper::idHelp()
+       for (int j = 0 ; j < jointField.size(); j++ )
+ 	{
+ 	  set<IDField*> & jf = jointField[j];
+-	  set<IDField*>::iterator j = jf.begin();
++	  set<IDField*>::iterator j2 = jf.begin();
+ 	  PP->printLOG(" { ");
+-	  while ( j != jf.end() )
++	  while ( j2 != jf.end() )
+ 	    {
+-	      PP->printLOG( (*j)->name + " " );
+-	      ++j;
++	      PP->printLOG( (*j2)->name + " " );
++	      ++j2;
+ 	    }
+ 	  PP->printLOG(" }");
+ 	}
diff --git a/biology/plink/patches/patch-sets.cpp b/biology/plink/patches/patch-sets.cpp
new file mode 100644
index 00000000000..70263c3b8fe
--- /dev/null
+++ b/biology/plink/patches/patch-sets.cpp
@@ -0,0 +1,20 @@
+$NetBSD: patch-sets.cpp,v 1.1 2012/11/16 00:32:07 joerg Exp $
+
+--- sets.cpp.orig	2012-11-15 12:39:15.000000000 +0000
++++ sets.cpp
+@@ -768,11 +768,11 @@ vector_t Set::profileTestScore()
+       //////////////////////////////////////////////
+       // Reset original missing status
+ 
+-      vector<Individual*>::iterator i = PP->sample.begin();
+-      while ( i != PP->sample.end() )
++      vector<Individual*>::iterator i2 = PP->sample.begin();
++      while ( i2 != PP->sample.end() )
+ 	{
+-	  (*i)->missing = (*i)->flag;
+-	  ++i;
++	  (*i2)->missing = (*i2)->flag;
++	  ++i2;
+ 	}
+ 
+       ////////////////////////////////////////////////