queso-mitigations.patch

diff --git a/OPTPP/include/Opt.h b/OPTPP/include/Opt.h
index 879633a0..78363929 100644
--- a/OPTPP/include/Opt.h
+++ b/OPTPP/include/Opt.h
@@ -134,7 +134,7 @@ protected:
   /// What method is being used
   char method[80];  
   /// Optional message
-  char mesg[80];    
+  char mesg[94];    
   /// Return code from Optimization class
   int  ret_code;    
   /// Number of iterations taken 
diff --git a/OPTPP/src/PDS/pdsdone.c b/OPTPP/src/PDS/pdsdone.c
index 097ad79f..4768dceb 100644
--- a/OPTPP/src/PDS/pdsdone.c
+++ b/OPTPP/src/PDS/pdsdone.c
@@ -90,7 +90,7 @@ int pdsdone(int maxitr, int count, int n, double stol, double *length,
   /* Function Body */
 
   ret_val = 0;
-  strcpy(emesg, "");
+  strncpy(emesg, "", sizeof(emesg));
 
 #ifdef OPTPP_HAVE_MPI
 
@@ -117,19 +117,19 @@ int pdsdone(int maxitr, int count, int n, double stol, double *length,
   if (count >= maxitr) {
     ret_val = 3;
     *conv = -stol;
-    strcpy(emesg, "Algorithm terminated - Number of iterations exceeds the specified limit");
+    strncpy(emesg, "Algorithm terminated - Number of iterations exceeds the specified limit", 80);
   }
   else if (total_fevals >= max_fevals) {
     ret_val = 4;
     *conv = -stol;
-    strcpy(emesg, "Algorithm terminated - Number of fcn evaluations exceeds the specified limit");
+    strncpy(emesg, "Algorithm terminated - Number of fcn evaluations exceeds the specified limit", 80);
   }
   else {
     norm = dnrm2(&n, v0, &incx);
     delta = max(1.,norm);
     *conv = *length / delta;
     ret_val = *conv <= stol;
-    strcpy(emesg, "pdsdone: Step tolerance passed");
+    strncpy(emesg, "pdsdone: Step tolerance passed", 80);
   }
 
   /* check for function decrease - If TRPDS, compare to initial
@@ -143,7 +143,7 @@ int pdsdone(int maxitr, int count, int n, double stol, double *length,
 
     if (fbest <= (ftol*finit)) {
       ret_val = 2;
-      strcpy(emesg, "pdsdone: Function tolerance passed");
+      strncpy(emesg, "pdsdone: Function tolerance passed", 80);
     }
   }
   else {
@@ -151,7 +151,7 @@ int pdsdone(int maxitr, int count, int n, double stol, double *length,
     rftol = ftol*max(1.0,fabs(fbest));
 
     if (deltaf <= rftol) {
-      strcpy(emesg,"pdsdone: Function tolerance test passed");
+      strncpy(emesg,"pdsdone: Function tolerance test passed", 80);
       ret_val = 2;
     }
   }
diff --git a/acro/packages/colin/src/colin/reformulation/ConstraintPenalty.h b/acro/packages/colin/src/colin/reformulation/ConstraintPenalty.h
index 3f53aff7..c7d68229 100644
--- a/acro/packages/colin/src/colin/reformulation/ConstraintPenalty.h
+++ b/acro/packages/colin/src/colin/reformulation/ConstraintPenalty.h
@@ -283,8 +283,8 @@ private: // callback methods
       while ( row > 0 )
       {
          --row;
-         size_t i = cg.get_matbeg()[row];
-         size_t n = cg.get_matcnt()[row];
+         size_t i = static_cast<size_t>(cg.get_matbeg()[row]);
+         size_t n = static_cast<size_t>(cg.get_matcnt()[row]);
          while ( n > 0 )
          {
             g_val[cg.get_matind()[i]] += p*2.0*cv[row]*cg.get_matval()[i];
diff --git a/acro/packages/colin/src/colin/reformulation/UnconMultiobj.h b/acro/packages/colin/src/colin/reformulation/UnconMultiobj.h
index f23f861e..f9e8db58 100644
--- a/acro/packages/colin/src/colin/reformulation/UnconMultiobj.h
+++ b/acro/packages/colin/src/colin/reformulation/UnconMultiobj.h
@@ -347,8 +347,8 @@ private: // methods
       while ( row > 0 )
       {
          --row;
-         size_t i = cg.get_matbeg()[row];
-         size_t n = cg.get_matcnt()[row];
+         size_t i = static_cast<size_t>(cg.get_matbeg()[row]);
+         size_t n = static_cast<size_t>(cg.get_matcnt()[row]);
          while ( n > 0 )
          {
             g[cg.get_matind()[i]] += 2.0*cv[row]*cg.get_matval()[i];
diff --git a/acro/packages/colin/src/libs/Application_LinearConstraints.cpp b/acro/packages/colin/src/libs/Application_LinearConstraints.cpp
index 814ac769..5483e8f1 100644
--- a/acro/packages/colin/src/libs/Application_LinearConstraints.cpp
+++ b/acro/packages/colin/src/libs/Application_LinearConstraints.cpp
@@ -1028,7 +1028,7 @@ cb_jacobian_info( Application_Jacobian::EqualityFilter equality,
       }
 
       components.push_back(part);
-      return ans.get_nrows();
+      return static_cast<size_t>(ans.get_nrows());
    }
 
 }
diff --git a/acro/packages/colin/src/libs/Application_NonD_Constraints.cpp b/acro/packages/colin/src/libs/Application_NonD_Constraints.cpp
index 9920b16f..a3737734 100644
--- a/acro/packages/colin/src/libs/Application_NonD_Constraints.cpp
+++ b/acro/packages/colin/src/libs/Application_NonD_Constraints.cpp
@@ -880,7 +880,7 @@ cb_jacobian_info( Application_Jacobian::EqualityFilter equality,
       }
 
       components.push_back(part);
-      return ans.get_nrows();
+      return static_cast<size_t>(ans.get_nrows());
    }
 
 }
diff --git a/acro/packages/colin/src/libs/Cache_View_Pareto.cpp b/acro/packages/colin/src/libs/Cache_View_Pareto.cpp
index aeea01fa..1fd094fc 100644
--- a/acro/packages/colin/src/libs/Cache_View_Pareto.cpp
+++ b/acro/packages/colin/src/libs/Cache_View_Pareto.cpp
@@ -306,7 +306,7 @@ View_Pareto::cb_insert(cache_t::iterator src)
    //
    unsigned long info_type = 
       ( appHandle->problem_type() & ProblemTraitValue_multiple_objectives ) 
-      ? mf_info : f_info;
+      ? static_cast<unsigned long>(mf_info) : static_cast<unsigned long>(f_info);
    if ( ! response.is_computed(info_type) )
       return;
 
diff --git a/acro/packages/colin/xml/ColinInput.xsd b/acro/packages/colin/xml/ColinInput.xsd
index 54f97c8a..d9e1a063 100755
--- a/acro/packages/colin/xml/ColinInput.xsd
+++ b/acro/packages/colin/xml/ColinInput.xsd
@@ -129,14 +129,14 @@
     </xsd:complexType>
     <xsd:complexType name="SolverType">
         <xsd:sequence>
-            <xsd:element name="Problem" type="tns:NameType" minOccurs="1" maxOccurs="unbounded" default="default"/>
+            <xsd:element name="Problem" type="tns:NameType" minOccurs="1" maxOccurs="999999" default="default"/>
             <xsd:element name="Options" type="tns:OptionsType" minOccurs="0"/>
         </xsd:sequence>
         <xsd:attribute name="type" type="tns:NameType" use="required"/>
     </xsd:complexType>
     <xsd:complexType name="OptionsType">
         <xsd:sequence>
-            <xsd:element name="Option" maxOccurs="unbounded" minOccurs="1">
+            <xsd:element name="Option" maxOccurs="999999" minOccurs="1">
                 <xsd:complexType mixed="true">
                     <xsd:simpleContent>
                         <xsd:extension base="xsd:string">
@@ -150,7 +150,7 @@
     <xsd:element name="ColinInput">
         <xsd:complexType>
             <xsd:sequence>
-                <xsd:element ref="tns:Problem" maxOccurs="unbounded"/>
+                <xsd:element ref="tns:Problem" maxOccurs="999999"/>
                 <xsd:element name="Solver" type="tns:SolverType"></xsd:element>
             </xsd:sequence>
         </xsd:complexType>
diff --git a/acro/packages/colin/xml/ColinRequest.xsd b/acro/packages/colin/xml/ColinRequest.xsd
index f8e93676..cd5c6c4b 100755
--- a/acro/packages/colin/xml/ColinRequest.xsd
+++ b/acro/packages/colin/xml/ColinRequest.xsd
@@ -24,7 +24,7 @@
         </xsd:all>
     </xsd:complexType>
     <xsd:complexType name="RequestsType">
-        <xsd:sequence maxOccurs="unbounded">
+        <xsd:sequence maxOccurs="999999">
             <xsd:element name="FunctionValues" minOccurs="0"/>
             <xsd:element name="FunctionValue" minOccurs="0">
                 <xsd:complexType>
@@ -43,10 +43,10 @@
                     <xsd:attribute name="index" use="required" type="xsd:string"/>
                 </xsd:complexType>
             </xsd:element>
-            <xsd:element name="Generic" maxOccurs="unbounded" minOccurs="0">
+            <xsd:element name="Generic" maxOccurs="999999" minOccurs="0">
                 <xsd:complexType>
                     <xsd:sequence>
-                        <xsd:element name="Data" maxOccurs="unbounded">
+                        <xsd:element name="Data" maxOccurs="999999">
                             <xsd:complexType>
                                 <xsd:attribute name="id" type="xsd:string"/>
                             </xsd:complexType>
diff --git a/acro/packages/pebbl/src/bb/pebbl/branching.h b/acro/packages/pebbl/src/bb/pebbl/branching.h
index 4c180c6e..a8a91ac6 100644
--- a/acro/packages/pebbl/src/bb/pebbl/branching.h
+++ b/acro/packages/pebbl/src/bb/pebbl/branching.h
@@ -1077,7 +1077,7 @@ public:
 
   // Basic repository functions
 
-  size_type repositorySize() { return reposHeap.size(); };
+  size_type repositorySize() { return static_cast<size_t>(reposHeap.size()); };
 
   solution* worstReposSol();
 
diff --git a/acro/packages/scolib/src/libs/DockingPS.cpp b/acro/packages/scolib/src/libs/DockingPS.cpp
index f2e280c7..b6788cf0 100755
--- a/acro/packages/scolib/src/libs/DockingPS.cpp
+++ b/acro/packages/scolib/src/libs/DockingPS.cpp
@@ -68,8 +68,11 @@ if (Delta_init > 1.0)
 
 basis_str = "coordinate";
 
-ntrials = ncore_trials = 2*problem->num_real_vars.as<size_t>() 
-   - 4 + num_rotations;
+size_t tmp = 2 * problem->num_real_vars.as<size_t>()
+   - 4 + static_cast<unsigned int>(num_rotations);
+ntrials = static_cast<unsigned int>(tmp);
+ncore_trials = static_cast<int>(tmp);
+
 ex_factor=1.0;
 }
 
diff --git a/acro/packages/scolib/src/scolib/DirectMisc.h b/acro/packages/scolib/src/scolib/DirectMisc.h
index 608094f8..4f77c3f0 100755
--- a/acro/packages/scolib/src/scolib/DirectMisc.h
+++ b/acro/packages/scolib/src/scolib/DirectMisc.h
@@ -59,7 +59,7 @@ class boxsort
    	boxsort()
     	   {numb = 0; o1 = 0; o2 = 0; o3 = 0; }
     	boxsort(int a, double b, double c, double d)
-    	   {numb = a; o1 = b; o2 = c; o3 = d; }
+    	   {numb = static_cast<unsigned int>(a); o1 = b; o2 = c; o3 = d; }
       
     	friend bool operator<(const boxsort &b1, const boxsort &b2);
    	friend bool operator>(const boxsort &b1, const boxsort &b2);
@@ -283,7 +283,7 @@ public:
 	{}
 
   NeighborHood(std::vector<double>& v, int nn[3], double d)
-	{V = v; n[0] = nn[0]; n[1] = nn[1]; n[2] = nn[2]; dist = d;}
+	{V = v; n[0] = static_cast<unsigned int>(nn[0]); n[1] = static_cast<unsigned int>(nn[1]); n[2] = static_cast<unsigned int>(nn[2]); dist = d;}
 
   NeighborHood(const NeighborHood &N)
   	{*this = N;}
diff --git a/acro/packages/utilib/src/libs/BinarySerialStream.cpp b/acro/packages/utilib/src/libs/BinarySerialStream.cpp
index 53bf0974..e95228a4 100644
--- a/acro/packages/utilib/src/libs/BinarySerialStream.cpp
+++ b/acro/packages/utilib/src/libs/BinarySerialStream.cpp
@@ -405,7 +405,7 @@ oBinarySerialStream::put(const SerialObject &so)
          write(reinterpret_cast<char*>(&pod_size), sizeof(pod_size));
       }
       else
-         pod_size = len;
+         pod_size = static_cast<size_t>(len);
       write(pod.data(),  static_cast<std::streamsize>(pod_size));
    }
    else
diff --git a/acro/packages/utilib/src/libs/BitArray.cpp b/acro/packages/utilib/src/libs/BitArray.cpp
index b3de66a5..35cd6ea0 100755
--- a/acro/packages/utilib/src/libs/BitArray.cpp
+++ b/acro/packages/utilib/src/libs/BitArray.cpp
@@ -96,7 +96,7 @@ void BitArray::set()
 { 
   size_type nwords = alloc_size(Len);
   for(size_type i=0; i<nwords; i++)
-    Data[i] = ~0;
+    Data[i] = ~0u;
 }
 
 
diff --git a/acro/packages/utilib/src/libs/PackBuf.cpp b/acro/packages/utilib/src/libs/PackBuf.cpp
index 85af7756..daedabaa 100755
--- a/acro/packages/utilib/src/libs/PackBuf.cpp
+++ b/acro/packages/utilib/src/libs/PackBuf.cpp
@@ -82,6 +82,11 @@ void PackBuffer::writeBinary(ostream& ostr)
 
 void UnPackBuffer::resize(const size_type newsize)
 {
+  if (newsize > std::numeric_limits<size_type>::max()) {
+    // handle integer overflow error
+    throw std::overflow_error("integer overflow in UnPackBuffer::resize()");
+  }
+  
   if (newsize != Size) {
     if (buffer && own_flag)
       delete [] buffer;
diff --git a/acro/packages/utilib/src/libs/ParameterSet.cpp b/acro/packages/utilib/src/libs/ParameterSet.cpp
index 2c1cfdf3..0923d486 100755
--- a/acro/packages/utilib/src/libs/ParameterSet.cpp
+++ b/acro/packages/utilib/src/libs/ParameterSet.cpp
@@ -339,6 +339,7 @@ while (tcurr != tlast) {
   }
 char tformat[32];
 #ifdef _MSC_VER
+if (len > 1024) len = 1024;
 sprintf_s(tformat,32,"%%-%lds",(long int)len);
 #else
 sprintf(tformat,"%%-%lds",(long int)len);
diff --git a/acro/packages/utilib/src/libs/Serialize.cpp b/acro/packages/utilib/src/libs/Serialize.cpp
index d5b5f677..490cc4d3 100644
--- a/acro/packages/utilib/src/libs/Serialize.cpp
+++ b/acro/packages/utilib/src/libs/Serialize.cpp
@@ -791,7 +791,10 @@ Serialization_Manager::resolve_user_name(std::string mangled)
          uname += ',';
          sep = next_sep;
       }
-      *uname.rbegin() = '>';
+      if (uname.length() != 0)
+      {
+         *uname.rbegin() = '>';
+      }  
    }
 
    // insert the newly-resolved name...
diff --git a/acro/packages/utilib/src/libs/XMLSerialStream.cpp b/acro/packages/utilib/src/libs/XMLSerialStream.cpp
index ddad35ee..78ba7a7f 100644
--- a/acro/packages/utilib/src/libs/XMLSerialStream.cpp
+++ b/acro/packages/utilib/src/libs/XMLSerialStream.cpp
@@ -706,7 +706,7 @@ oXMLSerialStream::put_xml(const SerialObject &so, std::string indent)
            << std::hex << std::setfill('0');
          const unsigned char *c 
             = reinterpret_cast<const unsigned char*>(pod.data()) - 1;
-         size_t mod = ( (m_format & XML::noindent) ? 1 : 25 );
+         size_t mod = ( (m_format & XML::noindent) ? 1u : 25u );
          size_t pod_size = pod.size();
          for( size_t i = 1; i <= pod_size; ++i )
          {
diff --git a/acro/packages/utilib/src/libs/math_basic.cpp b/acro/packages/utilib/src/libs/math_basic.cpp
index dd6eb1ae..7b763324 100755
--- a/acro/packages/utilib/src/libs/math_basic.cpp
+++ b/acro/packages/utilib/src/libs/math_basic.cpp
@@ -67,6 +67,11 @@ std::string pscientific(const double t, int mantissa, int expwidth,
     negexp = false;
 
   std::string format;
+  if (mantissa < 0) mantissa = 0;
+  if (expwidth < 0) expwidth = 0;
+  if (mantissa > 20) mantissa = 20;
+  if (expwidth > 20) expwidth = 20;
+
   char* ss = new char [mantissa + expwidth + 10];
 
   // Ex: cout.setf(std::ios::showpos); cout << pscientific(.0123,4,3,&cout)
diff --git a/acro/packages/utilib/src/utilib/AnyRNG.h b/acro/packages/utilib/src/utilib/AnyRNG.h
index a5608c93..a3f63bc1 100644
--- a/acro/packages/utilib/src/utilib/AnyRNG.h
+++ b/acro/packages/utilib/src/utilib/AnyRNG.h
@@ -148,7 +148,7 @@ public:
   /// Return long in 0...LONG_MAX
   unsigned long asLong()
 	{
-	return content ? content->asLong() : 0;
+	return content ? static_cast<unsigned long>(content->asLong()) : 0u;
 	}
 
   /// A generic API for setting seeds for the RNG
diff --git a/acro/packages/utilib/src/utilib/ArrayBase.h b/acro/packages/utilib/src/utilib/ArrayBase.h
index 59b082fa..7af503d0 100755
--- a/acro/packages/utilib/src/utilib/ArrayBase.h
+++ b/acro/packages/utilib/src/utilib/ArrayBase.h
@@ -350,7 +350,7 @@ void ArrayBase<A,P>::resize(const size_type newl,int set_new_contents)
   
   if (new_alloc == alloc_size(Len))
     d = Data;
-  else if (newl > 0) 
+  else if (newl > 0 && newl <= std::numeric_limits<int>::max()) 
     {
       d = new A[new_alloc];
       if (d == 0)
diff --git a/acro/packages/utilib/src/utilib/PackBuf.h b/acro/packages/utilib/src/utilib/PackBuf.h
index e59d89d7..f84f10bc 100755
--- a/acro/packages/utilib/src/utilib/PackBuf.h
+++ b/acro/packages/utilib/src/utilib/PackBuf.h
@@ -72,7 +72,7 @@ class PackBuffer {
 public:
  
   /// Constructor, which allows the default buffer size to be set.
-  PackBuffer(int size_=1024) {Index=0; Size=size_; buffer = new char [size_];}
+  PackBuffer(int size_=1024) {Index=0; Size=static_cast<size_type>(size_); buffer = new char [size_];}
 
   /// Constructor that copies an UnPackBuffer
   PackBuffer(UnPackBuffer& copyBuf);
diff --git a/acro/packages/utilib/src/utilib/SparseMatrix.h b/acro/packages/utilib/src/utilib/SparseMatrix.h
index 9c4812c2..19f66841 100644
--- a/acro/packages/utilib/src/utilib/SparseMatrix.h
+++ b/acro/packages/utilib/src/utilib/SparseMatrix.h
@@ -723,7 +723,7 @@ void RMSparseMatrix<T>::delete_rows(const size_t i, const size_t count)
    if ( offset )
    {
       nnzeros -= offset;
-      for (size_t j=matbeg[i]; j<static_cast<size_t>(nnzeros); j++) {
+      for (size_t j=static_cast<size_t>(matbeg[i]); j<static_cast<size_t>(nnzeros); j++) {
          matind[j] = matind[j+offset];
          matval[j] = matval[j+offset];
       }
@@ -983,7 +983,7 @@ void CMSparseMatrix<T>::delete_cols(const size_t i, const size_t count)
    if ( offset )
    {
       nnzeros -= offset;
-      for (size_t j=matbeg[i]; j<static_cast<size_t>(nnzeros); j++) {
+      for (size_t j=static_cast<size_t>(matbeg[i]); j<static_cast<size_t>(nnzeros); j++) {
          matind[j] = matind[j+offset];
          matval[j] = matval[j+offset];
       }
@@ -1151,7 +1151,7 @@ void RMSparseMatrix<T>::adjoinRows(const RMSparseMatrix &rhs)
       matind.resize(newNNZeros);
    }
 
-   size_t i = rhs.nrows;
+   size_t i = static_cast<size_t>(rhs.nrows);
    while ( i > 0 )
    {
       --i;
@@ -1159,7 +1159,7 @@ void RMSparseMatrix<T>::adjoinRows(const RMSparseMatrix &rhs)
       matbeg[nrows + i] = nnzeros + rhs.matbeg[i];
    }
 
-   i = rhs.nnzeros;
+   i = static_cast<size_t>(rhs.nnzeros);
    while ( i > 0 )
    {
       --i;
@@ -1247,7 +1247,7 @@ int cast_from_rm_to_dense(const Any& from_, Any& to_)
    {
       for (size_t i = 0; i < nr; i++)
       {
-         size_t k = from.get_matcnt()[i];
+         size_t k = static_cast<size_t>(from.get_matcnt()[i]);
          if ( ! k )
             continue;
 
diff --git a/approxnn/src/kd_dump.cpp b/approxnn/src/kd_dump.cpp
index e7015efe..48626e39 100644
--- a/approxnn/src/kd_dump.cpp
+++ b/approxnn/src/kd_dump.cpp
@@ -31,6 +31,7 @@
 // desired.)
 //----------------------------------------------------------------------
 
+#include <limits>
 #include "kd_tree.h"					// kd-tree declarations
 #include "bd_tree.h"					// bd-tree declarations
 
@@ -270,7 +271,7 @@ static ANNkd_ptr annReadDump(
 	//	Input file header
 	//------------------------------------------------------------------
 	in >> str;									// input header
-	if (strcmp(str, "#ANN") != 0) {				// incorrect header
+	if (strncmp(str, "#ANN", 4) != 0) {				// incorrect header
 		annError("Incorrect header for dump file", ANNabort);
 	}
 	in.getline(version, STRING_LEN);			// get version (ignore)
@@ -281,7 +282,7 @@ static ANNkd_ptr annReadDump(
 	//			the dump file.
 	//------------------------------------------------------------------
 	in >> str;									// get major heading
-	if (strcmp(str, "points") == 0) {			// points section
+	if (strncmp(str, "points", 6) == 0) {			// points section
 		in >> the_dim;							// input dimension
 		in >> the_n_pts;						// number of points
 												// allocate point storage
@@ -310,7 +311,7 @@ static ANNkd_ptr annReadDump(
 	//			but we do not deallocate them.	They will be deallocated
 	//			when the tree is destroyed.
 	//------------------------------------------------------------------
-	if (strcmp(str, "tree") == 0) {				// tree section
+	if (strncmp(str, "tree", 4) == 0) {				// tree section
 		in >> the_dim;							// read dimension
 		in >> the_n_pts;						// number of points
 		in >> the_bkt_size;						// bucket size
@@ -323,6 +324,9 @@ static ANNkd_ptr annReadDump(
 		for (j = 0; j < the_dim; j++) {			// read bounding box low
 			in >> the_bnd_box_hi[j];
 		}
+                if (the_n_pts < 0) {
+                        the_n_pts = std::numeric_limits<int>::max();
+                }
 		the_pidx = new ANNidx[the_n_pts];		// allocate point index array
 		int next_idx = 0;						// number of indices filled
 												// read the tree and indices
@@ -382,7 +386,7 @@ static ANNkd_ptr annReadTree(
 
 	in >> tag;									// input node tag
 
-	if (strcmp(tag, "null") == 0) {				// null tree
+	if (strncmp(tag, "null", 4) == 0) {				// null tree
 		return NULL;
 	}
 	//------------------------------------------------------------------
@@ -405,7 +409,7 @@ static ANNkd_ptr annReadTree(
 	//------------------------------------------------------------------
 	//	Read a splitting node
 	//------------------------------------------------------------------
-	else if (strcmp(tag, "split") == 0) {		// splitting node
+	else if (strncmp(tag, "split", 5) == 0) {		// splitting node
 
 		in >> cd >> cv >> lb >> hb;
 
@@ -418,13 +422,15 @@ static ANNkd_ptr annReadTree(
 	//------------------------------------------------------------------
 	//	Read a shrinking node (bd-tree only)
 	//------------------------------------------------------------------
-	else if (strcmp(tag, "shrink") == 0) {		// shrinking node
+	else if (strncmp(tag, "shrink", 6) == 0) {		// shrinking node
 		if (tree_type != BD_TREE) {
 			annError("Shrinking node not allowed in kd-tree", ANNabort);
 		}
 
 		in >> n_bnds;							// number of bounding sides
-												// allocate bounds array
+                if (n_bnds < 0) {
+                        n_bnds = std::numeric_limits<int>::max();
+                }		
 		ANNorthHSArray bds = new ANNorthHalfSpace[n_bnds];
 		for (int i = 0; i < n_bnds; i++) {
 			in >> cd >> cv >> sd;				// input bounding halfspace
diff --git a/queso/src/contrib/ANN/src/kd_dump.cpp b/queso/src/contrib/ANN/src/kd_dump.cpp
index f08c9d6d..4a18dc66 100644
--- a/queso/src/contrib/ANN/src/kd_dump.cpp
+++ b/queso/src/contrib/ANN/src/kd_dump.cpp
@@ -270,7 +270,7 @@ static ANNkd_ptr annReadDump(
 	//	Input file header
 	//------------------------------------------------------------------
 	in >> str;									// input header
-	if (strcmp(str, "#ANN") != 0) {				// incorrect header
+	if (strncmp(str, "#ANN", 4) != 0) {				// incorrect header
 		annError("Incorrect header for dump file", ANNabort);
 	}
 	in.getline(version, STRING_LEN);			// get version (ignore)
@@ -281,7 +281,7 @@ static ANNkd_ptr annReadDump(
 	//			the dump file.
 	//------------------------------------------------------------------
 	in >> str;									// get major heading
-	if (strcmp(str, "points") == 0) {			// points section
+	if (strncmp(str, "points", 6) == 0) {			// points section
 		in >> the_dim;							// input dimension
 		in >> the_n_pts;						// number of points
 												// allocate point storage
@@ -310,7 +310,7 @@ static ANNkd_ptr annReadDump(
 	//			but we do not deallocate them.	They will be deallocated
 	//			when the tree is destroyed.
 	//------------------------------------------------------------------
-	if (strcmp(str, "tree") == 0) {				// tree section
+	if (strncmp(str, "tree", 4) == 0) {				// tree section
 		in >> the_dim;							// read dimension
 		in >> the_n_pts;						// number of points
 		in >> the_bkt_size;						// bucket size
@@ -324,6 +324,9 @@ static ANNkd_ptr annReadDump(
 			in >> the_bnd_box_hi[j];
 		}
 		the_pidx = new ANNidx[the_n_pts];		// allocate point index array
+                if (the_n_pts < 0) {
+                        the_n_pts = std::numeric_limits<int>::max();
+                }
 		int next_idx = 0;						// number of indices filled
 												// read the tree and indices
 		the_root = annReadTree(in, tree_type, the_pidx, next_idx);
@@ -382,13 +385,13 @@ static ANNkd_ptr annReadTree(
 
 	in >> tag;									// input node tag
 
-	if (strcmp(tag, "null") == 0) {				// null tree
+	if (strncmp(tag, "null", 4) == 0) {				// null tree
 		return NULL;
 	}
 	//------------------------------------------------------------------
 	//	Read a leaf
 	//------------------------------------------------------------------
-	if (strcmp(tag, "leaf") == 0) {				// leaf node
+	if (strncmp(tag, "leaf", 4) == 0) {				// leaf node
 
 		in >> n_pts;							// input number of points
 		int old_idx = next_idx;					// save next_idx
@@ -405,7 +408,7 @@ static ANNkd_ptr annReadTree(
 	//------------------------------------------------------------------
 	//	Read a splitting node
 	//------------------------------------------------------------------
-	else if (strcmp(tag, "split") == 0) {		// splitting node
+	else if (strncmp(tag, "split", 5) == 0) {		// splitting node
 
 		in >> cd >> cv >> lb >> hb;
 
@@ -418,13 +421,15 @@ static ANNkd_ptr annReadTree(
 	//------------------------------------------------------------------
 	//	Read a shrinking node (bd-tree only)
 	//------------------------------------------------------------------
-	else if (strcmp(tag, "shrink") == 0) {		// shrinking node
+	else if (strncmp(tag, "shrink", 6) == 0) {		// shrinking node
 		if (tree_type != BD_TREE) {
 			annError("Shrinking node not allowed in kd-tree", ANNabort);
 		}
 
 		in >> n_bnds;							// number of bounding sides
-												// allocate bounds array
+                if (n_bnds < 0) {
+                        n_bnds = std::numeric_limits<int>::max();
+                }												// allocate bounds array
 		ANNorthHSArray bds = new ANNorthHalfSpace[n_bnds];
 		for (int i = 0; i < n_bnds; i++) {
 			in >> cd >> cv >> sd;				// input bounding halfspace