diff -Nru shogun-3.2.0/debian/changelog shogun-3.2.0/debian/changelog
--- shogun-3.2.0/debian/changelog	2014-10-21 03:23:59.000000000 +0000
+++ shogun-3.2.0/debian/changelog	2016-07-28 19:12:37.000000000 +0000
@@ -1,3 +1,9 @@
+shogun (3.2.0-7.3+rpi1) stretch-staging; urgency=medium
+
+  * Apply patch from Debian bts to fix build with eigen 3.3 (Closes: 809290)
+
+ -- Peter Michael Green <plugwash@raspbian.org>  Thu, 28 Jul 2016 19:12:05 +0000
+
 shogun (3.2.0-7.3) unstable; urgency=medium
 
   * Non-maintainer upload.
diff -Nru shogun-3.2.0/debian/patches/eigen3.3.patch shogun-3.2.0/debian/patches/eigen3.3.patch
--- shogun-3.2.0/debian/patches/eigen3.3.patch	1970-01-01 00:00:00.000000000 +0000
+++ shogun-3.2.0/debian/patches/eigen3.3.patch	2016-07-28 19:11:41.000000000 +0000
@@ -0,0 +1,166 @@
+Description: Fix build with Eigen 3.3
+Origin: upstream, https://github.com/shogun-toolbox/shogun/commit/57cd0958b153accf12f535ab9406dc8511bf22ec
+Bug: https://github.com/shogun-toolbox/shogun/issues/3140
+Bug: https://github.com/shogun-toolbox/shogun/issues/3141
+Bug-Debian: https://bugs.debian.org/809290
+Author: Viktor Gal <viktor.gal@maeth.com>
+Last-Update: 2016-05-18
+--- a/src/shogun/lib/tapkee/defines.hpp
++++ b/src/shogun/lib/tapkee/defines.hpp
+@@ -49,12 +49,12 @@
+ 		TapkeeOutput(const tapkee::DenseMatrix& e, const tapkee::ProjectingFunction& p) :
+ 			embedding(), projection(p)
+ 		{
+-			embedding.swap(e);
++			embedding = e;
+ 		}
+ 		TapkeeOutput(const TapkeeOutput& that) :
+ 			embedding(), projection(that.projection)
+ 		{
+-			this->embedding.swap(that.embedding);
++			this->embedding = that.embedding;
+ 		}
+ 		tapkee::DenseMatrix embedding;
+ 		tapkee::ProjectingFunction projection;
+--- a/src/shogun/mathematics/eigen3.h
++++ b/src/shogun/mathematics/eigen3.h
+@@ -62,6 +62,13 @@
+ 
+ 	#endif	//EIGEN_VERSION_AT_LEAST(3,0,93)
+ 
++#if ((EIGEN_WORLD_VERSION == 3) && (EIGEN_MAJOR_VERSION == 2) && \
++	((EIGEN_MINOR_VERSION == 91) || (EIGEN_MINOR_VERSION == 92)))
++	// Regression has been introduced to eigen develop (3.3alpha1+):
++	// http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1229
++	// until this is not fixed we need to copy the matrix and calculate the log
++	#define EIGEN_WITH_LOG_BUG_1229 1
++#endif
+ namespace shogun
+ {
+ template<class T> class SGSparseMatrix;
+--- a/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
++++ b/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
+@@ -64,7 +64,12 @@
+ 	Map<MatrixXd> mat(m.matrix, m.num_rows, m.num_cols);
+ 	SGMatrix<float64_t> log_m(m.num_rows, m.num_cols);
+ 	Map<MatrixXd> log_mat(log_m.matrix, log_m.num_rows, log_m.num_cols);
++#if EIGEN_WITH_LOG_BUG_1229
++	MatrixXd tmp = mat;
++	log_mat=tmp.log();
++#else
+ 	log_mat=mat.log();
++#endif
+ 
+ 	// the log(C) is also a linear operator here
+ 	// reset the operator of this function with log(C)
+--- a/tests/unit/lib/computation/SerialComputationEngine_unittest.cc
++++ b/tests/unit/lib/computation/SerialComputationEngine_unittest.cc
+@@ -41,7 +41,12 @@
+ 	mat(1,1)=3.0;
+ 	Map<MatrixXd> m(mat.matrix, mat.num_rows, mat.num_cols);
+ 	Map<MatrixXd> log_m(log_mat.matrix, log_mat.num_rows, log_mat.num_cols);
++#if EIGEN_WITH_LOG_BUG_1229
++	MatrixXd tmp = m;
++	log_m=tmp.log();
++#else
+ 	log_m=m.log();
++#endif
+ 
+ 	// create linear operator and aggregator
+ 	CDenseMatrixOperator<float64_t>* log_op=new CDenseMatrixOperator<float64_t>(log_mat);
+--- a/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc
++++ b/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc
+@@ -39,7 +39,12 @@
+ 	mat(1,1)=3.0;
+ 	Map<MatrixXd> m(mat.matrix, mat.num_rows, mat.num_cols);
+ 	Map<MatrixXd> log_m(log_mat.matrix, log_mat.num_rows, log_mat.num_cols);
++#if EIGEN_WITH_LOG_BUG_1229
++	MatrixXd tmp = m;
++	log_m=tmp.log();
++#else
+ 	log_m=m.log();
++#endif
+ 
+ 	// create linear operator and aggregator
+ 	CDenseMatrixOperator<float64_t>* log_op=new CDenseMatrixOperator<float64_t>(log_mat);
+--- a/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc
++++ b/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc
+@@ -185,7 +185,12 @@
+ #if EIGEN_VERSION_AT_LEAST(3,1,0)
+ 	// compute the trace of log(m) using Eigen3 that uses Schur-Parlett algorithm
+ 	Map<MatrixXd> eig_m(m.matrix, m.num_rows, m.num_cols);
++#if EIGEN_WITH_LOG_BUG_1229
++	MatrixXd tmp = eig_m;
++	float64_t trace_log_m=tmp.log().diagonal().sum();
++#else
+ 	float64_t trace_log_m=eig_m.log().diagonal().sum();
++#endif
+ #else
+ 	float64_t trace_log_m=-11.51292546497021618279;
+ #endif // EIGEN_VERSION_AT_LEAST(3,1,0)
+@@ -367,7 +372,12 @@
+ #if EIGEN_VERSION_AT_LEAST(3,1,0)
+ 	// compute the trace of log(m) using Eigen3 that uses Schur-Parlett algorithm
+ 	Map<MatrixXd> eig_m(m.matrix, m.num_rows, m.num_cols);
++#if EIGEN_WITH_LOG_BUG_1229
++	MatrixXd tmp = eig_m;
++	float64_t trace_log_m=tmp.log().diagonal().sum();
++#else
+ 	float64_t trace_log_m=eig_m.log().diagonal().sum();
++#endif
+ #else
+ 	float64_t trace_log_m=-11.51292546497021618279;
+ #endif // EIGEN_VERSION_AT_LEAST(3,1,0)
+--- a/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc
++++ b/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc
+@@ -220,33 +220,37 @@
+ 
+ TEST(SparseMatrixOperator, get_sparsity_structure)
+ {
+-	const int size=9;
+-	const int max_pow=10;
++	const int32_t size=9;
++	const int32_t max_pow=10;
+ 
+-	SGMatrix<double> m(size, size);
++	SGMatrix<float64_t> m(size, size);
+ 
+ 	m.set_const(0.0);
+-	for (int i=0; i<size; ++i)
++	for (int32_t i=0; i<size; ++i)
+ 		m(i,i)=2.0;
+-	for (int i=0; i<size; i+=4)
++	for (int32_t i=0; i<size; i+=4)
+ 		m(i,size-1)=2.0;
+-	for (int i=0; i<size; i+=4)
++	for (int32_t i=0; i<size; i+=4)
+ 		m(size-1,i)=2.0;
+ 
+-	CSparseFeatures<double> feat(m);
+-	SGSparseMatrix<double> sm=feat.get_sparse_feature_matrix();
+-	CSparseMatrixOperator<double> op(sm);
++	CSparseFeatures<float64_t> feat(m);
++	SGSparseMatrix<float64_t> sm=feat.get_sparse_feature_matrix();
++	CSparseMatrixOperator<float64_t> op(sm);
+ 	CSparseMatrixOperator<bool>* b_op
+ 		=static_cast<CSparseMatrixOperator<bool>*>(op);
+ 
+-	SparseMatrix<bool, RowMajor, int> sp
++	SparseMatrix<bool, RowMajor, int32_t> sp
+ 		=EigenSparseUtil<bool>::toEigenSparse(b_op->get_matrix_operator());
+-	SparseMatrix<double, RowMajor, int> sm2
+-		=EigenSparseUtil<double>::toEigenSparse(sm);
++	SparseMatrix<float64_t, RowMajor, int32_t> sm2
++		=EigenSparseUtil<float64_t>::toEigenSparse(sm);
+ 
+ 	// compute direct matrix power and then the sparsity structure
+-	for (int i=2; i<=max_pow; ++i)
++	for (int32_t i=2; i<=max_pow; ++i)
++#if EIGEN_VERSION_AT_LEAST(3,2,91)
++		sp=(sp.cast<float64_t>()*sm2).cast<bool>();
++#else
+ 		sp=sp*sm2;
++#endif
+ 
+ 	int32_t* outerIndexPtr=const_cast<int32_t*>(sp.outerIndexPtr());
+ 	int32_t* innerIndexPtr=const_cast<int32_t*>(sp.innerIndexPtr());
diff -Nru shogun-3.2.0/debian/patches/series shogun-3.2.0/debian/patches/series
--- shogun-3.2.0/debian/patches/series	2014-07-07 14:56:42.000000000 +0000
+++ shogun-3.2.0/debian/patches/series	2016-07-28 19:11:52.000000000 +0000
@@ -1 +1,3 @@
 disable_sse.diff
+eigen3.3.patch
+