Patch out C++ bugs in plink

Also force dynamic linking so it picks up libz.

plink-1.07_install

@@ -33,6 +33,11 @@ then
   unzip $temp_dir/${APPNAME}-${VERSION}-src.zip
 
   cd ${APPNAME}-${VERSION}-src
+  cp /shared/ucl/apps/build_scripts/plink-patches/*.patch .
+  for a in `ls *.patch`
+  do
+    patch < $a
+  done
   make
 else
   echo "Hash mismatch."

plink-patches/Makefile.patch

@@ -0,0 +1,11 @@
+--- Makefile.old	2015-07-21 13:23:55.000000000 +0100
++++ Makefile	2015-07-21 13:15:01.000000000 +0100
+@@ -27,7 +27,7 @@
+ FORCE_32BIT = 
+ WITH_ZLIB = 1
+ WITH_LAPACK = 
+-FORCE_DYNAMIC = 
++FORCE_DYNAMIC = 1
+
+ # Put C++ compiler here; Windows has it's own specific version
+ CXX_UNIX = g++

plink-patches/elf.cpp.patch

@@ -0,0 +1,25 @@
+--- elf.cpp.old	2015-07-21 13:02:42.000000000 +0100
++++ elf.cpp	2015-07-21 13:03:24.000000000 +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 it3 = chr_cnt.begin();
++      while ( it3 != chr_cnt.end() )
+ 	{
+-	  int c = i->first;
++	  int c = it3->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;
++	  ++it3;
+ 	}
+
+     }

plink-patches/idhelp.cpp.patch

@@ -0,0 +1,19 @@
+--- idhelp.cpp.old	2015-07-21 13:04:26.000000000 +0100
++++ idhelp.cpp	2015-07-21 13:09:25.000000000 +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 it1 = jf.begin();
+ 	  PP->printLOG(" { ");
+-	  while ( j != jf.end() )
++	  while ( it1 != jf.end() )
+ 	    {
+-	      PP->printLOG( (*j)->name + " " );
+-	      ++j;
++	      PP->printLOG( (*it1)->name + " " );
++	      ++it1;
+ 	    }
+ 	  PP->printLOG(" }");
+ 	}

plink-patches/sets.cpp.patch

@@ -0,0 +1,18 @@
+--- sets.cpp.old	2015-07-21 12:58:06.000000000 +0100
++++ sets.cpp	2015-07-21 13:01:36.000000000 +0100
+@@ -768,11 +768,11 @@
+       //////////////////////////////////////////////
+       // Reset original missing status
+
+-      vector<Individual*>::iterator i = PP->sample.begin();
+-      while ( i != PP->sample.end() )
++      vector<Individual*>::iterator it2 = PP->sample.begin();
++      while ( it2 != PP->sample.end() )
+ 	{
+-	  (*i)->missing = (*i)->flag;
+-	  ++i;
++	  (*it2)->missing = (*it2)->flag;
++	  ++it2;
+ 	}
+
+       ////////////////////////////////////////////////