Use Eigen2 2.0 head version rather then 2.0.6. It contains various bug fix.

extern/Eigen2/Eigen/src/Array/Functors.h

@@ -43,6 +43,8 @@ struct ei_scalar_add_op {
   inline const PacketScalar packetOp(const PacketScalar& a) const
   { return ei_padd(a, ei_pset1(m_other)); }
   const Scalar m_other;
+private:
+  ei_scalar_add_op& operator=(const ei_scalar_add_op&);
 };
 template<typename Scalar>
 struct ei_functor_traits<ei_scalar_add_op<Scalar> >
@@ -138,6 +140,8 @@ struct ei_scalar_pow_op {
   inline ei_scalar_pow_op(const Scalar& exponent) : m_exponent(exponent) {}
   inline Scalar operator() (const Scalar& a) const { return ei_pow(a, m_exponent); }
   const Scalar m_exponent;
+private:
+  ei_scalar_pow_op& operator=(const ei_scalar_pow_op&);
 };
 template<typename Scalar>
 struct ei_functor_traits<ei_scalar_pow_op<Scalar> >

extern/Eigen2/Eigen/src/Array/PartialRedux.h

@@ -133,6 +133,8 @@ struct ei_member_redux {
   inline result_type operator()(const MatrixBase<Derived>& mat) const
   { return mat.redux(m_functor); }
   const BinaryOp m_functor;
+private:
+  ei_member_redux& operator=(const ei_member_redux&);
 };
 
 /** \array_module \ingroup Array
@@ -290,6 +292,9 @@ template<typename ExpressionType, int Direction> class PartialRedux
 
   protected:
     ExpressionTypeNested m_matrix;
+
+  private:
+    PartialRedux& operator=(const PartialRedux&);
 };
 
 /** \array_module

extern/Eigen2/Eigen/src/Core/CommaInitializer.h

@@ -116,6 +116,9 @@ struct CommaInitializer
   int m_row;              // current row id
   int m_col;              // current col id
   int m_currentBlockRows; // current block height
+
+private:
+  CommaInitializer& operator=(const CommaInitializer&);
 };
 
 /** \anchor MatrixBaseCommaInitRef

extern/Eigen2/Eigen/src/Core/Cwise.h

@@ -178,6 +178,9 @@ template<typename ExpressionType> class Cwise
 
   protected:
     ExpressionTypeNested m_matrix;
+
+  private:
+    Cwise& operator=(const Cwise&);
 };
 
 /** \returns a Cwise wrapper of *this providing additional coefficient-wise operations

extern/Eigen2/Eigen/src/Core/Flagged.h

@@ -109,6 +109,9 @@ template<typename ExpressionType, unsigned int Added, unsigned int Removed> clas
 
   protected:
     ExpressionTypeNested m_matrix;
+
+private:
+  Flagged& operator=(const Flagged&);
 };
 
 /** \returns an expression of *this with added flags

extern/Eigen2/Eigen/src/Core/Functors.h

@@ -279,6 +279,8 @@ struct ei_scalar_multiple_op {
   EIGEN_STRONG_INLINE const PacketScalar packetOp(const PacketScalar& a) const
   { return ei_pmul(a, ei_pset1(m_other)); }
   const Scalar m_other;
+private:
+  ei_scalar_multiple_op& operator=(const ei_scalar_multiple_op&);
 };
 template<typename Scalar>
 struct ei_functor_traits<ei_scalar_multiple_op<Scalar> >
@@ -294,6 +296,8 @@ struct ei_scalar_quotient1_impl {
   EIGEN_STRONG_INLINE const PacketScalar packetOp(const PacketScalar& a) const
   { return ei_pmul(a, ei_pset1(m_other)); }
   const Scalar m_other;
+private:
+  ei_scalar_quotient1_impl& operator=(const ei_scalar_quotient1_impl&);
 };
 template<typename Scalar>
 struct ei_functor_traits<ei_scalar_quotient1_impl<Scalar,true> >
@@ -306,6 +310,8 @@ struct ei_scalar_quotient1_impl<Scalar,false> {
   EIGEN_STRONG_INLINE ei_scalar_quotient1_impl(const Scalar& other) : m_other(other) {}
   EIGEN_STRONG_INLINE Scalar operator() (const Scalar& a) const { return a / m_other; }
   const Scalar m_other;
+private:
+  ei_scalar_quotient1_impl& operator=(const ei_scalar_quotient1_impl&);
 };
 template<typename Scalar>
 struct ei_functor_traits<ei_scalar_quotient1_impl<Scalar,false> >
@@ -323,6 +329,8 @@ template<typename Scalar>
 struct ei_scalar_quotient1_op : ei_scalar_quotient1_impl<Scalar, NumTraits<Scalar>::HasFloatingPoint > {
   EIGEN_STRONG_INLINE ei_scalar_quotient1_op(const Scalar& other)
     : ei_scalar_quotient1_impl<Scalar, NumTraits<Scalar>::HasFloatingPoint >(other) {}
+private:
+  ei_scalar_quotient1_op& operator=(const ei_scalar_quotient1_op&);
 };
 
 // nullary functors
@@ -335,6 +343,8 @@ struct ei_scalar_constant_op {
   EIGEN_STRONG_INLINE const Scalar operator() (int, int = 0) const { return m_other; }
   EIGEN_STRONG_INLINE const PacketScalar packetOp() const { return ei_pset1(m_other); }
   const Scalar m_other;
+private:
+  ei_scalar_constant_op& operator=(const ei_scalar_constant_op&);
 };
 template<typename Scalar>
 struct ei_functor_traits<ei_scalar_constant_op<Scalar> >

extern/Eigen2/Eigen/src/Core/Matrix.h

@@ -505,7 +505,9 @@ class Matrix
     template<typename OtherDerived>
     EIGEN_STRONG_INLINE Matrix& _set(const MatrixBase<OtherDerived>& other)
     {
-      _set_selector(other.derived(), typename ei_meta_if<bool(int(OtherDerived::Flags) & EvalBeforeAssigningBit), ei_meta_true, ei_meta_false>::ret());
+      // this enum introduced to fix compilation with gcc 3.3
+      enum { cond = int(OtherDerived::Flags) & EvalBeforeAssigningBit };
+      _set_selector(other.derived(), typename ei_meta_if<bool(cond), ei_meta_true, ei_meta_false>::ret());
       return *this;
     }
 

extern/Eigen2/Eigen/src/Core/NestByValue.h

@@ -100,6 +100,9 @@ template<typename ExpressionType> class NestByValue
 
   protected:
     const ExpressionType m_expression;
+
+  private:
+    NestByValue& operator=(const NestByValue&);
 };
 
 /** \returns an expression of the temporary version of *this.

extern/Eigen2/Eigen/src/Core/Part.h

@@ -124,8 +124,10 @@ template<typename MatrixType, unsigned int Mode> class Part
     }
 
   protected:
-
     const typename MatrixType::Nested m_matrix;
+
+  private:
+    Part& operator=(const Part&);
 };
 
 /** \nonstableyet

extern/Eigen2/Eigen/src/Core/Swap.h

@@ -117,6 +117,9 @@ template<typename ExpressionType> class SwapWrapper
 
   protected:
     ExpressionType& m_expression;
+
+  private:
+    SwapWrapper& operator=(const SwapWrapper&);
 };
 
 /** swaps *this with the expression \a other.

extern/Eigen2/Eigen/src/Core/util/Memory.h

@@ -1,5 +1,5 @@
 // This file is part of Eigen, a lightweight C++ template library
-// for linear algebra. Eigen itself is part of the KDE project.
+// for linear algebra.
 //
 // Copyright (C) 2008 Gael Guennebaud <g.gael@free.fr>
 // Copyright (C) 2008-2009 Benoit Jacob <jacob.benoit.1@gmail.com>
@@ -27,7 +27,17 @@
 #ifndef EIGEN_MEMORY_H
 #define EIGEN_MEMORY_H
 
-#if defined(__APPLE__) || defined(_WIN64)
+// FreeBSD 6 seems to have 16-byte aligned malloc
+// See http://svn.freebsd.org/viewvc/base/stable/6/lib/libc/stdlib/malloc.c?view=markup
+// FreeBSD 7 seems to have 16-byte aligned malloc except on ARM and MIPS architectures
+// See http://svn.freebsd.org/viewvc/base/stable/7/lib/libc/stdlib/malloc.c?view=markup
+#if defined(__FreeBSD__) && !defined(__arm__) && !defined(__mips__)
+#define EIGEN_FREEBSD_MALLOC_ALREADY_ALIGNED 1
+#else
+#define EIGEN_FREEBSD_MALLOC_ALREADY_ALIGNED 0
+#endif
+
+#if defined(__APPLE__) || defined(_WIN64) || EIGEN_FREEBSD_MALLOC_ALREADY_ALIGNED
   #define EIGEN_MALLOC_ALREADY_ALIGNED 1
 #else
   #define EIGEN_MALLOC_ALREADY_ALIGNED 0
@@ -65,7 +75,7 @@ inline void ei_handmade_aligned_free(void *ptr)
 }
 
 /** \internal allocates \a size bytes. The returned pointer is guaranteed to have 16 bytes alignment.
-  * On allocation error, the returned pointer is undefined, but if exceptions are enabled then a std::bad_alloc is thrown.
+  * On allocation error, the returned pointer is null, and if exceptions are enabled then a std::bad_alloc is thrown.
   */
 inline void* ei_aligned_malloc(size_t size)
 {
@@ -96,7 +106,7 @@ inline void* ei_aligned_malloc(size_t size)
 }
 
 /** allocates \a size bytes. If Align is true, then the returned ptr is 16-byte-aligned.
-  * On allocation error, the returned pointer is undefined, but if exceptions are enabled then a std::bad_alloc is thrown.
+  * On allocation error, the returned pointer is null, and if exceptions are enabled then a std::bad_alloc is thrown.
   */
 template<bool Align> inline void* ei_conditional_aligned_malloc(size_t size)
 {
@@ -116,20 +126,29 @@ template<> inline void* ei_conditional_aligned_malloc<false>(size_t size)
   return result;
 }
 
+/** \internal construct the elements of an array.
+  * The \a size parameter tells on how many objects to call the constructor of T.
+  */
+template<typename T> inline T* ei_construct_elements_of_array(T *ptr, size_t size)
+{
+  for (size_t i=0; i < size; ++i) ::new (ptr + i) T;
+  return ptr;
+}
+
 /** allocates \a size objects of type T. The returned pointer is guaranteed to have 16 bytes alignment.
   * On allocation error, the returned pointer is undefined, but if exceptions are enabled then a std::bad_alloc is thrown.
   * The default constructor of T is called.
   */
 template<typename T> inline T* ei_aligned_new(size_t size)
 {
-  void *void_result = ei_aligned_malloc(sizeof(T)*size);
-  return ::new(void_result) T[size];
+  T *result = reinterpret_cast<T*>(ei_aligned_malloc(sizeof(T)*size));
+  return ei_construct_elements_of_array(result, size);
 }
 
 template<typename T, bool Align> inline T* ei_conditional_aligned_new(size_t size)
 {
-  void *void_result = ei_conditional_aligned_malloc<Align>(sizeof(T)*size);
-  return ::new(void_result) T[size];
+  T *result = reinterpret_cast<T*>(ei_conditional_aligned_malloc<Align>(sizeof(T)*size));
+  return ei_construct_elements_of_array(result, size);
 }
 
 /** \internal free memory allocated with ei_aligned_malloc
@@ -163,10 +182,10 @@ template<> inline void ei_conditional_aligned_free<false>(void *ptr)
   free(ptr);
 }
 
-/** \internal delete the elements of an array.
+/** \internal destruct the elements of an array.
   * The \a size parameters tells on how many objects to call the destructor of T.
   */
-template<typename T> inline void ei_delete_elements_of_array(T *ptr, size_t size)
+template<typename T> inline void ei_destruct_elements_of_array(T *ptr, size_t size)
 {
   // always destruct an array starting from the end.
   while(size) ptr[--size].~T();
@@ -177,7 +196,7 @@ template<typename T> inline void ei_delete_elements_of_array(T *ptr, size_t size
   */
 template<typename T> inline void ei_aligned_delete(T *ptr, size_t size)
 {
-  ei_delete_elements_of_array<T>(ptr, size);
+  ei_destruct_elements_of_array<T>(ptr, size);
   ei_aligned_free(ptr);
 }
 
@@ -186,7 +205,7 @@ template<typename T> inline void ei_aligned_delete(T *ptr, size_t size)
   */
 template<typename T, bool Align> inline void ei_conditional_aligned_delete(T *ptr, size_t size)
 {
-  ei_delete_elements_of_array<T>(ptr, size);
+  ei_destruct_elements_of_array<T>(ptr, size);
   ei_conditional_aligned_free<Align>(ptr);
 }
 
@@ -225,8 +244,8 @@ inline static int ei_alignmentOffset(const Scalar* ptr, int maxOffset)
   #define ei_aligned_stack_free(PTR,SIZE) ei_aligned_free(PTR)
 #endif
 
-#define ei_aligned_stack_new(TYPE,SIZE) ::new(ei_aligned_stack_alloc(sizeof(TYPE)*SIZE)) TYPE[SIZE]
-#define ei_aligned_stack_delete(TYPE,PTR,SIZE) do {ei_delete_elements_of_array<TYPE>(PTR, SIZE); \
+#define ei_aligned_stack_new(TYPE,SIZE) ei_construct_elements_of_array(reinterpret_cast<TYPE*>(ei_aligned_stack_alloc(sizeof(TYPE)*SIZE)), SIZE)
+#define ei_aligned_stack_delete(TYPE,PTR,SIZE) do {ei_destruct_elements_of_array<TYPE>(PTR, SIZE); \
                                                    ei_aligned_stack_free(PTR,sizeof(TYPE)*SIZE);} while(0)
 
 
@@ -244,7 +263,7 @@ inline static int ei_alignmentOffset(const Scalar* ptr, int maxOffset)
         return Eigen::ei_conditional_aligned_malloc<NeedsToAlign>(size); \
       }
   #endif
-  
+
   #define EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign) \
       void *operator new(size_t size) { \
         return Eigen::ei_conditional_aligned_malloc<NeedsToAlign>(size); \

extern/Eigen2/Eigen/src/SVD/SVD.h

@@ -107,6 +107,7 @@ void SVD<MatrixType>::compute(const MatrixType& matrix)
   const int m = matrix.rows();
   const int n = matrix.cols();
   const int nu = std::min(m,n);
+  ei_assert(m>=n && "In Eigen 2.0, SVD only works for MxN matrices with M>=N. Sorry!");
 
   m_matU.resize(m, nu);
   m_matU.setZero();

extern/Eigen2/Eigen/src/Sparse/AmbiVector.h

@@ -99,6 +99,8 @@ template<typename _Scalar> class AmbiVector
       allocSize = allocSize/sizeof(Scalar) + (allocSize%sizeof(Scalar)>0?1:0);
       Scalar* newBuffer = new Scalar[allocSize];
       memcpy(newBuffer,  m_buffer,  copyElements * sizeof(ListEl));
+      delete[] m_buffer;
+      m_buffer = newBuffer;
     }
 
   protected:
@@ -238,8 +240,11 @@ Scalar& AmbiVector<Scalar>::coeffRef(int i)
       else
       {
         if (m_llSize>=m_allocatedElements)
+        {
           reallocateSparse();
-        ei_internal_assert(m_llSize<m_size && "internal error: overflow in sparse mode");
+          llElements = reinterpret_cast<ListEl*>(m_buffer);
+        }
+        ei_internal_assert(m_llSize<m_allocatedElements && "internal error: overflow in sparse mode");
         // let's insert a new coefficient
         ListEl& el = llElements[m_llSize];
         el.value = Scalar(0);
@@ -365,6 +370,9 @@ class AmbiVector<_Scalar>::Iterator
     int m_cachedIndex;          // current coordinate
     Scalar m_cachedValue;       // current value
     bool m_isDense;             // mode of the vector
+
+  private:
+    Iterator& operator=(const Iterator&);
 };
 
 

extern/Eigen2/Eigen/src/Sparse/DynamicSparseMatrix.h

@@ -289,9 +289,11 @@ class DynamicSparseMatrix<Scalar,_Flags>::InnerIterator : public SparseVector<Sc
     inline int row() const { return IsRowMajor ? m_outer : Base::index(); }
     inline int col() const { return IsRowMajor ? Base::index() : m_outer; }
 
-
   protected:
     const int m_outer;
+
+  private:
+    InnerIterator& operator=(const InnerIterator&);
 };
 
 #endif // EIGEN_DYNAMIC_SPARSEMATRIX_H

extern/Eigen2/Eigen/src/Sparse/SparseBlock.h

@@ -53,6 +53,9 @@ class SparseInnerVectorSet : ei_no_assignment_operator,
         inline InnerIterator(const SparseInnerVectorSet& xpr, int outer)
           : MatrixType::InnerIterator(xpr.m_matrix, xpr.m_outerStart + outer)
         {}
+
+      private:
+        InnerIterator& operator=(const InnerIterator&);
     };
 
     inline SparseInnerVectorSet(const MatrixType& matrix, int outerStart, int outerSize)
@@ -110,6 +113,8 @@ class SparseInnerVectorSet<DynamicSparseMatrix<_Scalar, _Options>, Size>
         inline InnerIterator(const SparseInnerVectorSet& xpr, int outer)
           : MatrixType::InnerIterator(xpr.m_matrix, xpr.m_outerStart + outer)
         {}
+      private:
+        InnerIterator& operator=(const InnerIterator&);
     };
 
     inline SparseInnerVectorSet(const MatrixType& matrix, int outerStart, int outerSize)

extern/Eigen2/Eigen/src/Sparse/SparseCwise.h

@@ -156,6 +156,9 @@ template<typename ExpressionType> class SparseCwise
 
   protected:
     ExpressionTypeNested m_matrix;
+
+  private:
+    SparseCwise& operator=(const SparseCwise&);
 };
 
 template<typename Derived>

extern/Eigen2/Eigen/src/Sparse/SparseCwiseBinaryOp.h

@@ -126,6 +126,8 @@ class SparseCwiseBinaryOp<BinaryOp,Lhs,Rhs>::InnerIterator
     EIGEN_STRONG_INLINE InnerIterator(const SparseCwiseBinaryOp& binOp, int outer)
       : Base(binOp,outer)
     {}
+  private:
+    InnerIterator& operator=(const InnerIterator&);
 };
 
 /***************************************************************************
@@ -197,6 +199,9 @@ class ei_sparse_cwise_binary_op_inner_iterator_selector<BinaryOp, Lhs, Rhs, Deri
     const BinaryOp& m_functor;
     Scalar m_value;
     int m_id;
+
+  private:
+    ei_sparse_cwise_binary_op_inner_iterator_selector& operator=(const ei_sparse_cwise_binary_op_inner_iterator_selector&);
 };
 
 // sparse - sparse  (product)
@@ -250,6 +255,9 @@ class ei_sparse_cwise_binary_op_inner_iterator_selector<ei_scalar_product_op<T>,
     LhsIterator m_lhsIter;
     RhsIterator m_rhsIter;
     const BinaryFunc& m_functor;
+
+  private:
+    ei_sparse_cwise_binary_op_inner_iterator_selector& operator=(const ei_sparse_cwise_binary_op_inner_iterator_selector&);
 };
 
 // sparse - dense  (product)
@@ -290,6 +298,9 @@ class ei_sparse_cwise_binary_op_inner_iterator_selector<ei_scalar_product_op<T>,
     LhsIterator m_lhsIter;
     const BinaryFunc m_functor;
     const int m_outer;
+
+  private:
+    ei_sparse_cwise_binary_op_inner_iterator_selector& operator=(const ei_sparse_cwise_binary_op_inner_iterator_selector&);
 };
 
 // sparse - dense  (product)

extern/Eigen2/Eigen/src/Sparse/SparseCwiseUnaryOp.h

@@ -90,6 +90,9 @@ class SparseCwiseUnaryOp<UnaryOp,MatrixType>::InnerIterator
   protected:
     MatrixTypeIterator m_iter;
     const UnaryOp m_functor;
+
+  private:
+    InnerIterator& operator=(const InnerIterator&);
 };
 
 template<typename Derived>

extern/Eigen2/Eigen/src/Sparse/SparseDiagonalProduct.h

@@ -120,6 +120,8 @@ class ei_sparse_diagonal_product_inner_iterator_selector
               const SparseDiagonalProductType& expr, int outer)
       : Base(expr.rhs().innerVector(outer) .cwise()* expr.lhs().diagonal(), 0)
     {}
+  private:
+    ei_sparse_diagonal_product_inner_iterator_selector& operator=(const ei_sparse_diagonal_product_inner_iterator_selector&);
 };
 
 template<typename Lhs, typename Rhs, typename SparseDiagonalProductType>

extern/Eigen2/Eigen/src/Sparse/SparseFlagged.h

@@ -64,16 +64,21 @@ template<typename ExpressionType, unsigned int Added, unsigned int Removed> clas
 
   protected:
     ExpressionTypeNested m_matrix;
+
+  private:
+    SparseFlagged& operator=(const SparseFlagged&);
 };
 
 template<typename ExpressionType, unsigned int Added, unsigned int Removed>
   class SparseFlagged<ExpressionType,Added,Removed>::InnerIterator : public ExpressionType::InnerIterator
 {
   public:
-
     EIGEN_STRONG_INLINE InnerIterator(const SparseFlagged& xpr, int outer)
       : ExpressionType::InnerIterator(xpr.m_matrix, outer)
     {}
+
+  private:
+    InnerIterator& operator=(const InnerIterator&);
 };
 
 template<typename ExpressionType, unsigned int Added, unsigned int Removed>

extern/Eigen2/Eigen/src/Sparse/SparseMatrix.h

@@ -259,19 +259,21 @@ class SparseMatrix
       m_data.resize(k,0);
     }
 
+    /** Resizes the matrix to a \a rows x \a cols matrix and initializes it to zero
+      * \sa resizeNonZeros(int), reserve(), setZero()
+      */
     void resize(int rows, int cols)
     {
-//       std::cerr << this << " resize " << rows << "x" << cols << "\n";
       const int outerSize = IsRowMajor ? rows : cols;
       m_innerSize = IsRowMajor ? cols : rows;
       m_data.clear();
-      if (m_outerSize != outerSize)
+      if (m_outerSize != outerSize || m_outerSize==0)
       {
         delete[] m_outerIndex;
         m_outerIndex = new int [outerSize+1];
         m_outerSize = outerSize;
-        memset(m_outerIndex, 0, (m_outerSize+1)*sizeof(int));
       }
+      memset(m_outerIndex, 0, (m_outerSize+1)*sizeof(int));
     }
     void resizeNonZeros(int size)
     {
@@ -442,6 +444,9 @@ class SparseMatrix<Scalar,_Flags>::InnerIterator
     int m_id;
     const int m_start;
     const int m_end;
+
+  private:
+    InnerIterator& operator=(const InnerIterator&);
 };
 
 #endif // EIGEN_SPARSEMATRIX_H

extern/Eigen2/Eigen/src/Sparse/SparseTranspose.h

@@ -62,15 +62,20 @@ template<typename MatrixType> class SparseTranspose
 
   protected:
     const typename MatrixType::Nested m_matrix;
+
+  private:
+    SparseTranspose& operator=(const SparseTranspose&);
 };
 
 template<typename MatrixType> class SparseTranspose<MatrixType>::InnerIterator : public MatrixType::InnerIterator
 {
   public:
-
     EIGEN_STRONG_INLINE InnerIterator(const SparseTranspose& trans, int outer)
       : MatrixType::InnerIterator(trans.m_matrix, outer)
     {}
+
+  private:
+    InnerIterator& operator=(const InnerIterator&);
 };
 
 template<typename MatrixType> class SparseTranspose<MatrixType>::ReverseInnerIterator : public MatrixType::ReverseInnerIterator

extern/Eigen2/Eigen/src/Sparse/SparseVector.h

@@ -360,6 +360,9 @@ class SparseVector<Scalar,_Flags>::InnerIterator
     const CompressedStorage<Scalar>& m_data;
     int m_id;
     const int m_end;
+
+  private:
+    InnerIterator& operator=(const InnerIterator&);
 };
 
 #endif // EIGEN_SPARSEVECTOR_H

extern/Eigen2/eigen-update.sh

@@ -17,7 +17,7 @@ if [ -d eigen2 ]
 then
     cd eigen2
     # put here the version you want to use
-    hg up 2.0.6
+    hg up 2.0
     rm -f `find Eigen/ -type f -name "CMakeLists.txt"`
     cp -r Eigen ..
     cd ..