Remove some compiler warnings and problems found with msvc-8

Code/GraphMol/RWMol.cpp

@@ -1,6 +1,6 @@
 // $Id$
 //
-//  Copyright (C) 2003-2006 Greg Landrum and Rational Discovery LLC
+//  Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
 //
 //   @@ All Rights Reserved  @@
 //
@@ -119,11 +119,15 @@ namespace RDKit{
     }
 
     // remove bonds attached to the atom
+    std::vector<std::pair<unsigned int,unsigned int> > nbrs;
     ADJ_ITER b1,b2;
     boost::tie(b1,b2)=getAtomNeighbors(oatom);
     while(b1!=b2){
-      removeBond(oatom->getIdx(),*b1);
-      b1++;
+      nbrs.push_back(std::make_pair(oatom->getIdx(),*b1));
+      ++b1;
+    }
+    for(unsigned int i=0;i<nbrs.size();++i){
+      removeBond(nbrs[i].first,nbrs[i].second);
     }
 
     // loop over all atoms with higher indices and update their indices

Code/GraphMol/RankAtoms.cpp

@@ -82,7 +82,8 @@ namespace RankAtoms{
 	  if(elem<2.-tol){
 	    accum *= valVect[j];
 	  } else {
-	    accum *= pow(valVect[j],static_cast<int>(elem));
+	    accum *= pow(static_cast<double>(valVect[j]),
+                         static_cast<int>(elem));
 	  }
 	}
       }

Code/GraphMol/RankAtoms.h

@@ -148,8 +148,7 @@ namespace RankAtoms {
 #endif
 
     INT_VECT idxVect;
-    idxVect.reserve(indicesInPlay.size());
-    std::copy(indicesInPlay.begin(),indicesInPlay.end(),idxVect.begin());
+    idxVect.assign(indicesInPlay.begin(),indicesInPlay.end());
 
     // -------------
     //

Code/Numerics/Vector.h

@@ -1,5 +1,5 @@
 //
-//  Copyright (C) 2004-2006 Rational Discovery LLC
+//  Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
 //
 //   @@ All Rights Reserved  @@
 //
@@ -13,8 +13,6 @@
 #include <iomanip>
 #include <cstdlib>
 #include <boost/random.hpp>
-#include <memory.h>
-#include <time.h>
 #include <boost/smart_ptr.hpp>
 
 namespace RDNumeric {

Code/RDGeneral/Invariant.cpp

@@ -1,6 +1,6 @@
 // $Id$
 //
-// Copyright (C) 2001-2006 Randal M. Henne and Rational Discovery LLC
+// Copyright (C) 2001-2008 Greg Landrum, Randal M. Henne, and Rational Discovery LLC
 // 
 //  @@ All Rights Reserved @@
 //
@@ -8,8 +8,8 @@
 #include "Invariant.h"
 
 #include <string>
-#include <stdio.h>
 #include <iostream>
+#include <boost/lexical_cast.hpp>
 
 namespace Invar {
 
@@ -22,10 +22,7 @@ namespace Invar {
   std::string& Invariant::
   toString()
   {
-    char 
-      line[10];
-
-    sprintf( line, "%d", this->getLine() );
+    std::string line=boost::lexical_cast<std::string>(this->getLine());
     
     stringRep_d += "\n" + this->getMessage() + "\nViolation occurred on line " 
       + line + " in file " + this->getFile() + "\nFailed Expression: "

Code/RDGeneral/Invariant.h

@@ -1,5 +1,5 @@
 //
-// Copyright (C)  2001-2006 Randal M. Henne and Rational Discovery LLC
+// Copyright (C)  2001-2008 Greg Landrum, Randal M. Henne and Rational Discovery LLC
 //
 //  @@ All Rights Reserved @@
 //
@@ -10,7 +10,6 @@
 #include <assert.h>
 #include <string>
 #include <iostream>
-#include <stdio.h>
 #include <stdexcept>
 
 #include <RDGeneral/RDLog.h>
@@ -129,8 +128,9 @@ namespace Invar {
      BOOST_LOG(rdErrorLog) << "\n\n****\n" << inv << "****\n\n"; throw inv;
 
 #define RANGE_CHECK( lo, x, hi ) if ( (lo)>(hi) || (x)<(lo) || (x)>(hi) ) {\
-     char expr[80]; sprintf( expr, "%lf <= %lf <= %lf", double(lo), double(x), double( hi ) );\
-     Invar::Invariant inv( "Range Error", #x, expr, __FILE__, __LINE__ );\
+     std::stringstream errstr;\
+     errstr << lo << " <= " << x <<" <= "<<hi;\
+     Invar::Invariant inv( "Range Error", #x, errstr.str().c_str(), __FILE__, __LINE__ );\
      BOOST_LOG(rdErrorLog) << "\n\n****\n" << inv << "****\n\n"; throw inv; }
 
 #define TEST_ASSERT( expr ) if ( !(expr) ) {\