Technical changes for R integration

Avoid including iostream (R complains about that). All output protected by
preprocessor directive (R checker should not see an instance of std::cout << in
your code). Also added getWassersteinCost to be in line with the Dionysus
implementation used in TDA.

14 files changed, 114 insertions, 39 deletions

diff --git a/geom_bottleneck/bottleneck/include/ANN/ANN.h b/geom_bottleneck/bottleneck/include/ANN/ANN.h
index cd48d8e..004dfe2 100644
--- a/geom_bottleneck/bottleneck/include/ANN/ANN.h
+++ b/geom_bottleneck/bottleneck/include/ANN/ANN.h
@@ -96,7 +96,6 @@
 
 #include <cstdlib>			// standard lib includes
 #include <cmath>			// math includes
-#include <iostream>			// I/O streams
 #include <cstring>			// C-style strings
 #include <vector>			 
 #include <assert.h>			 
@@ -130,6 +129,12 @@
 #define ANNcopyright	"David M. Mount and Sunil Arya"
 #define ANNlatestRev	"Jan 27, 2010"
 
+#include "def_debug_bt.h"
+
+#ifndef FOR_R_TDA
+#include <iostream>			// I/O streams
+#endif
+
 namespace geom_bt {
 //----------------------------------------------------------------------
 //	ANNbool
@@ -798,8 +803,10 @@ public:
 		int				bs = 1,			// bucket size
 		ANNsplitRule	split = ANN_KD_SUGGEST);	// splitting method
 
+#ifndef FOR_R_TDA
 	ANNkd_tree(							// build from dump file
 		std::istream&	in);			// input stream for dump file
+#endif
 
 	~ANNkd_tree();						// tree destructor
 
@@ -834,6 +841,7 @@ public:
 	ANNpointArray thePoints()			// return pointer to points
 		{  return pts;  }
 
+#ifndef FOR_R_TDA
 	virtual void Print(					// print the tree (for debugging)
 		ANNbool			with_pts,		// print points as well?
 		std::ostream&	out);			// output stream
@@ -841,6 +849,7 @@ public:
 	virtual void Dump(					// dump entire tree
 		ANNbool			with_pts,		// print points as well?
 		std::ostream&	out);			// output stream
+#endif
 								
 	virtual void getStats(				// compute tree statistics
 		ANNkdStats&		st);			// the statistics (modified)
@@ -885,8 +894,10 @@ public:
 		ANNsplitRule	split  = ANN_KD_SUGGEST,	// splitting rule
 		ANNshrinkRule	shrink = ANN_BD_SUGGEST);	// shrinking rule
 
+#ifndef FOR_R_TDA
 	ANNbd_tree(							// build from dump file
 		std::istream&	in);			// input stream for dump file
+#endif
 };
 
 //----------------------------------------------------------------------
diff --git a/geom_bottleneck/bottleneck/include/ANN/bd_tree.h b/geom_bottleneck/bottleneck/include/ANN/bd_tree.h
index 0791429..38cecb7 100644
--- a/geom_bottleneck/bottleneck/include/ANN/bd_tree.h
+++ b/geom_bottleneck/bottleneck/include/ANN/bd_tree.h
@@ -29,6 +29,7 @@
 
 #include <ANN/ANNx.h>					// all ANN includes
 #include "kd_tree.h"					// kd-tree includes
+#include "def_debug_bt.h"
 
 namespace geom_bt {
 //----------------------------------------------------------------------
@@ -91,7 +92,9 @@ public:
 				ANNkdStats &st,					// statistics
 				ANNorthRect &bnd_box);			// bounding box
 	virtual void print(int level, ostream &out);// print node
+#ifndef FOR_R_TDA
 	virtual void dump(ostream &out);			// dump node
+#endif
 
 	virtual void ann_search(ANNdist);			// standard search
 	virtual void ann_pri_search(ANNdist);		// priority search
diff --git a/geom_bottleneck/bottleneck/include/ANN/kd_tree.h b/geom_bottleneck/bottleneck/include/ANN/kd_tree.h
index 5fb362d..a1e53e5 100644
--- a/geom_bottleneck/bottleneck/include/ANN/kd_tree.h
+++ b/geom_bottleneck/bottleneck/include/ANN/kd_tree.h
@@ -31,6 +31,7 @@
 
 #include <utility>                      // for std::pair
 #include <ANN/ANNx.h>					// all ANN includes
+#include "def_debug_bt.h"
 
 using namespace std;					// make std:: available
 
@@ -73,7 +74,9 @@ public:
 				ANNorthRect &bnd_box) = 0;		// bounding box
 												// print node
 	virtual void print(int level, ostream &out) = 0;
+#ifndef FOR_R_TDA
 	virtual void dump(ostream &out) = 0;		// dump node
+#endif
 
 	friend class ANNkd_tree;					// allow kd-tree to access us
 
@@ -139,7 +142,9 @@ public:
 				ANNkdStats &st,					// statistics
 				ANNorthRect &bnd_box);			// bounding box
 	virtual void print(int level, ostream &out);// print node
+#ifndef FOR_R_TDA
 	virtual void dump(ostream &out);			// dump node
+#endif
 
 	virtual void ann_search(ANNdist);			// standard search
 	virtual void ann_pri_search(ANNdist);		// priority search
@@ -217,7 +222,9 @@ public:
 				ANNkdStats &st,					// statistics
 				ANNorthRect &bnd_box);			// bounding box
 	virtual void print(int level, ostream &out);// print node
+#ifndef FOR_R_TDA
 	virtual void dump(ostream &out);			// dump node
+#endif
 
 	virtual void ann_search(ANNdist);			// standard search
 	virtual void ann_pri_search(ANNdist);		// priority search
diff --git a/geom_bottleneck/bottleneck/include/basic_defs_bt.h b/geom_bottleneck/bottleneck/include/basic_defs_bt.h
index 5334b6d..759f18e 100644
--- a/geom_bottleneck/bottleneck/include/basic_defs_bt.h
+++ b/geom_bottleneck/bottleneck/include/basic_defs_bt.h
@@ -27,16 +27,20 @@
 #endif
 
 #include <vector>
+#include <stdexcept>
 #include <math.h>
 #include <cstddef>
 #include <unordered_map>
 #include <unordered_set>
-#include <iostream>
 #include <string>
 #include <assert.h>
 
 #include "def_debug_bt.h"
 
+#ifndef FOR_R_TDA
+#include <iostream>
+#endif
+
 
 namespace geom_bt {
 
@@ -50,7 +54,9 @@ struct Point {
     bool operator!=(const Point& other) const;
     Point(CoordinateType ax, CoordinateType ay) : x(ax), y(ay) {}
     Point() : x(0.0), y(0.0) {}
+#ifndef FOR_R_TDA
     friend std::ostream& operator<<(std::ostream& output, const Point p);
+#endif
 };
 
 struct DiagramPoint 
@@ -90,7 +96,9 @@ public:
             //return 0.5 * ( x + y);
     }
 
+#ifndef FOR_R_TDA
     friend std::ostream& operator<<(std::ostream& output, const DiagramPoint p);
+#endif
 };
 
 struct PointHash {
@@ -130,7 +138,9 @@ public:
     std::unordered_set<DiagramPoint, DiagramPointHash>::iterator end() { return points.end(); }
     std::unordered_set<DiagramPoint, DiagramPointHash>::const_iterator cbegin() const { return points.cbegin(); }
     std::unordered_set<DiagramPoint, DiagramPointHash>::const_iterator cend() const { return points.cend(); }
+#ifndef FOR_R_TDA
     friend std::ostream& operator<<(std::ostream& output, const DiagramPointSet& ps);
+#endif
     friend void addProjections(DiagramPointSet& A, DiagramPointSet& B);
     template<class PairIterator> DiagramPointSet(PairIterator first, PairIterator last);
     template<class PairIterator> void fillIn(PairIterator first, PairIterator last);
diff --git a/geom_bottleneck/bottleneck/include/bottleneck.h b/geom_bottleneck/bottleneck/include/bottleneck.h
index 19ae89a..3267c5d 100644
--- a/geom_bottleneck/bottleneck/include/bottleneck.h
+++ b/geom_bottleneck/bottleneck/include/bottleneck.h
@@ -22,7 +22,7 @@
 #define BOTTLENECK_H
 
 
-#include <iostream>
+//#include <iostream>
 #include <fstream>
 #include <vector>
 #include <algorithm>
diff --git a/geom_bottleneck/bottleneck/include/def_debug_bt.h b/geom_bottleneck/bottleneck/include/def_debug_bt.h
index eaf356d..60f834e 100644
--- a/geom_bottleneck/bottleneck/include/def_debug_bt.h
+++ b/geom_bottleneck/bottleneck/include/def_debug_bt.h
@@ -18,12 +18,16 @@
 
 */
 
-#ifndef DEF_DEBUG_H
-#define DEF_DEBUG_H
+#ifndef DEF_DEBUG_BT_H
+#define DEF_DEBUG_BT_H
 
 //#define DEBUG_BOUND_MATCH
 //#define DEBUG_NEIGHBOUR_ORACLE
 //#define DEBUG_MATCHING
 //#define DEBUG_AUCTION
+// This symbol should be defined only in the version
+// for R package TDA, to comply with some CRAN rules
+// like no usage of cout, cerr, cin, exit, etc.
+//#define FOR_R_TDA
 
 #endif
diff --git a/geom_bottleneck/bottleneck/src/ann/ANN.cpp b/geom_bottleneck/bottleneck/src/ann/ANN.cpp
index 7bae577..83c7ef6 100644
--- a/geom_bottleneck/bottleneck/src/ann/ANN.cpp
+++ b/geom_bottleneck/bottleneck/src/ann/ANN.cpp
@@ -30,9 +30,11 @@
 #include <ciso646>                      // make VS more conformal
 #endif
 
+#include <stdexcept>
 #include <cstdlib>						// C standard lib defs
 #include <ANN/ANNx.h>					// all ANN includes
 #include <ANN/ANNperf.h>				// ANN performance 
+#include "def_debug_bt.h"
 
 
 
@@ -80,10 +82,12 @@ void annPrintPt(						// print a point
 	int					dim,			// the dimension
 	std::ostream		&out)			// output stream
 {
+#ifndef FOR_R_TDA
 	for (int j = 0; j < dim; j++) {
 		out << pt[j];
 		if (j < dim-1) out << " ";
 	}
+#endif
 }
 
 //----------------------------------------------------------------------
@@ -197,11 +201,16 @@ bool ANNorthRect::intersects(const int dim, const ANNorthRect& r) const
 void annError(const char* msg, ANNerr level)
 {
 	if (level == ANNabort) {
+#ifndef FOR_R_TDA
 		cerr << "ANN: ERROR------->" << msg << "<-------------ERROR\n";
-		exit(1);
+#endif
+        throw std::runtime_error(std::string("ANN: Error: ") + std::string(msg));
+		//exit(1);
 	}
 	else {
+#ifndef FOR_R_TDA
 		cerr << "ANN: WARNING----->" << msg << "<-------------WARNING\n";
+#endif
 	}
 }
 
diff --git a/geom_bottleneck/bottleneck/src/ann/bd_tree.cpp b/geom_bottleneck/bottleneck/src/ann/bd_tree.cpp
index 8c1ef6d..a5dd69c 100644
--- a/geom_bottleneck/bottleneck/src/ann/bd_tree.cpp
+++ b/geom_bottleneck/bottleneck/src/ann/bd_tree.cpp
@@ -31,6 +31,7 @@
 #include "kd_split.h"					// kd-tree splitting rules
 
 #include <ANN/ANNperf.h>				// performance evaluation
+#include "def_debug_bt.h"
 
 namespace geom_bt {
 //----------------------------------------------------------------------
@@ -43,6 +44,7 @@ void ANNbd_shrink::print(				// print shrinking node
 		int level,						// depth of node in tree
 		ostream &out)					// output stream
 {
+#ifndef FOR_R_TDA
 	child[ANN_OUT]->print(level+1, out);		// print out-child
 
 	out << "    ";
@@ -61,6 +63,7 @@ void ANNbd_shrink::print(				// print shrinking node
 	out << "\n";
 
 	child[ANN_IN]->print(level+1, out);			// print in-child
+#endif
 }
 
 //----------------------------------------------------------------------
diff --git a/geom_bottleneck/bottleneck/src/ann/kd_dump.cpp b/geom_bottleneck/bottleneck/src/ann/kd_dump.cpp
index 64db9a7..ecaf7ea 100644
--- a/geom_bottleneck/bottleneck/src/ann/kd_dump.cpp
+++ b/geom_bottleneck/bottleneck/src/ann/kd_dump.cpp
@@ -33,6 +33,7 @@
 
 #include "kd_tree.h"					// kd-tree declarations
 #include "bd_tree.h"					// bd-tree declarations
+#include "def_debug_bt.h"
 
 using namespace std;					// make std:: available
 
@@ -101,6 +102,7 @@ namespace geom_bt {
 	//						... (repeated n_bnds times)
 	//----------------------------------------------------------------------
 
+#ifndef FOR_R_TDA
 	void ANNkd_tree::Dump(					// dump entire tree
 		ANNbool with_pts,				// print points as well?
 		ostream &out)					// output stream
@@ -132,20 +134,24 @@ namespace geom_bt {
 		}
 		out.precision(0);					// restore default precision
 	}
+#endif
 
 	void ANNkd_split::dump(					// dump a splitting node
 		ostream &out)					// output stream
 	{
+#ifndef FOR_R_TDA
 		out << "split " << cut_dim << " " << cut_val << " ";
 		out << cd_bnds[ANN_LO] << " " << cd_bnds[ANN_HI] << "\n";
 
 		child[ANN_LO]->dump(out);			// print low child
 		child[ANN_HI]->dump(out);			// print high child
+#endif
 	}
 
 	void ANNkd_leaf::dump(					// dump a leaf node
 		ostream &out)					// output stream
 	{
+#ifndef FOR_R_TDA
 		if (this == KD_TRIVIAL) {			// canonical trivial leaf node
 			out << "leaf 0\n";				// leaf no points
 		}
@@ -156,17 +162,20 @@ namespace geom_bt {
 			}
 			out << "\n";
 		}
+#endif
 	}
 
 	void ANNbd_shrink::dump(				// dump a shrinking node
 		ostream &out)					// output stream
 	{
+#ifndef FOR_R_TDA
 		out << "shrink " << n_bnds << "\n";
 		for (int j = 0; j < n_bnds; j++) {
 			out << bnds[j].cd << " " << bnds[j].cv << " " << bnds[j].sd << "\n";
 		}
 		child[ANN_IN]->dump(out);			// print in-child
 		child[ANN_OUT]->dump(out);			// print out-child
+#endif
 	}
 
 	//----------------------------------------------------------------------
@@ -441,7 +450,9 @@ namespace geom_bt {
 		}
 		else {
 			annError("Illegal node type in dump file", ANNabort);
+#ifndef FOR_R_TDA
 			exit(0);								// to keep the compiler happy
+#endif
 		}
 	}
 }
diff --git a/geom_bottleneck/bottleneck/src/ann/kd_tree.cpp b/geom_bottleneck/bottleneck/src/ann/kd_tree.cpp
index ad3a82d..e8f7f63 100644
--- a/geom_bottleneck/bottleneck/src/ann/kd_tree.cpp
+++ b/geom_bottleneck/bottleneck/src/ann/kd_tree.cpp
@@ -38,6 +38,7 @@
 #include "kd_split.h"					// kd-tree splitting rules
 #include "kd_util.h"					// kd-tree utilities
 #include <ANN/ANNperf.h>				// performance evaluation
+#include "def_debug_bt.h"
 
 namespace geom_bt {
 //----------------------------------------------------------------------
@@ -75,6 +76,7 @@ void ANNkd_split::print(				// print splitting node
 		int level,						// depth of node in tree
 		ostream &out)					// output stream
 {
+#ifndef FOR_R_TDA
 	child[ANN_HI]->print(level+1, out);	// print high child
 	out << "    ";
 	for (int i = 0; i < level; i++)		// print indentation
@@ -85,13 +87,14 @@ void ANNkd_split::print(				// print splitting node
 	out << " np=" << actual_num_points;
 	out << "\n";
 	child[ANN_LO]->print(level+1, out);	// print low child
+#endif
 }
 
 void ANNkd_leaf::print(					// print leaf node
 		int level,						// depth of node in tree
 		ostream &out)					// output stream
 {
-
+#ifndef FOR_R_TDA
 	out << "    ";
 	for (int i = 0; i < level; i++)		// print indentation
 		out << "..";
@@ -107,8 +110,10 @@ void ANNkd_leaf::print(					// print leaf node
 		}
 		out << ">\n";
 	}
+#endif
 }
 
+#ifndef FOR_R_TDA
 void ANNkd_tree::Print(					// print entire tree
 		ANNbool with_pts,				// print points as well?
 		ostream &out)					// output stream
@@ -128,6 +133,7 @@ void ANNkd_tree::Print(					// print entire tree
 		root->print(0, out);			// invoke printing at root
 	}
 }
+#endif
 
 //----------------------------------------------------------------------
 //	kd_tree statistics (for performance evaluation)
diff --git a/geom_bottleneck/bottleneck/src/basic_defs.cpp b/geom_bottleneck/bottleneck/src/basic_defs.cpp
index e09b119..76e6cc5 100644
--- a/geom_bottleneck/bottleneck/src/basic_defs.cpp
+++ b/geom_bottleneck/bottleneck/src/basic_defs.cpp
@@ -20,6 +20,7 @@
 
 #include <algorithm>
 #include <cfloat>
+#include "def_debug_bt.h"
 #include "basic_defs_bt.h"
 
 namespace geom_bt {
@@ -36,6 +37,7 @@ bool Point::operator!=(const Point& other) const
     return !(*this == other);
 }
 
+#ifndef FOR_R_TDA
 std::ostream& operator<<(std::ostream& output, const Point p)
 {
     output << "(" << p.x << ", " << p.y << ")";
@@ -51,6 +53,7 @@ std::ostream& operator<<(std::ostream& output, const PointSet& ps)
     output << "\b\b }";
     return output;
 }
+#endif
 
 double sqrDist(const Point& a, const Point& b)
 {
@@ -90,6 +93,7 @@ bool DiagramPoint::operator!=(const DiagramPoint& other) const
     return !(*this == other);
 }
 
+#ifndef FOR_R_TDA
 std::ostream& operator<<(std::ostream& output, const DiagramPoint p)
 {
     if ( p.type == DiagramPoint::DIAG ) {
@@ -109,6 +113,7 @@ std::ostream& operator<<(std::ostream& output, const DiagramPointSet& ps)
     output << "\b\b }";
     return output;
 }
+#endif
 
 DiagramPoint::DiagramPoint(double xx, double yy, Type ttype, IdType uid) : 
     x(xx),
@@ -116,14 +121,8 @@ DiagramPoint::DiagramPoint(double xx, double yy, Type ttype, IdType uid) :
     type(ttype),
     id(uid)
 {
-    //if ( xx < 0 )
-        //throw "Negative x coordinate";
-    //if ( yy < 0)
-        //throw "Negative y coordinate";
-    //if ( yy < xx )
-        //throw "Point is below the diagonal";
     if ( yy == xx and ttype != DiagramPoint::DIAG)
-        throw "Point on the main diagonal must have DIAG type";
+        throw std::runtime_error("Point on the main diagonal must have DIAG type");
 
 }
 
diff --git a/geom_bottleneck/bottleneck/src/bottleneck.cpp b/geom_bottleneck/bottleneck/src/bottleneck.cpp
index a5009c5..365995a 100644
--- a/geom_bottleneck/bottleneck/src/bottleneck.cpp
+++ b/geom_bottleneck/bottleneck/src/bottleneck.cpp
@@ -151,7 +151,7 @@ double bottleneckDistExact(DiagramPointSet& A, DiagramPointSet& B)
     const double approxDist = 0.5 * ( interval.first + interval.second);
     const double minDist = interval.first;
     const double maxDist = interval.second;
-    //std::cerr << std::setprecision(15) <<  "minDist = " << minDist << ", maxDist = " << maxDist << std::endl;
+    //std::cout << std::setprecision(15) <<  "minDist = " << minDist << ", maxDist = " << maxDist << std::endl;
     if ( delta == 0 ) {
         return interval.first;
     }
@@ -163,17 +163,17 @@ double bottleneckDistExact(DiagramPointSet& A, DiagramPointSet& B)
         pointsA.push_back(ptA);
     }
 
-    //std::vector<double> killDist;
-    //for(auto ptA : A) {
-        //for(auto ptB : B) {
-            //if ( distLInf(ptA, ptB) > minDist and distLInf(ptA, ptB) < maxDist) {
-                //killDist.push_back(distLInf(ptA, ptB));
-                //std::cout << ptA << ", " << ptB << std::endl;
+    //std::vector<double> killdist;
+    //for(auto pta : a) {
+        //for(auto ptb : b) {
+            //if ( distlinf(pta, ptb) > mindist and distlinf(pta, ptb) < maxdist) {
+                //killdist.push_back(distlinf(pta, ptb));
+                //std::cout << pta << ", " << ptb << std::endl;
             //}
         //}
     //}
-    //std::sort(killDist.begin(), killDist.end());
-    //for(auto d : killDist) {
+    //std::sort(killdist.begin(), killdist.end());
+    //for(auto d : killdist) {
         //std::cout << d << std::endl;
     //}
     //std::cout << "*************" << std::endl;
@@ -257,7 +257,7 @@ double bottleneckDistExact(DiagramPointSet& A, DiagramPointSet& B)
         
         std::sort(yCentersVec.begin(), yCentersVec.end(), compLambda);
 
-        //  std::cout << "Sorted vector of y-centers:" << std::endl;
+        // std::cout << "Sorted vector of y-centers:" << std::endl;
         //for(auto coordPtPair : yCentersVec) {
             //std::cout << coordPtPair.first << ", id = " << coordPtPair.second.id << std::endl;
         //}
@@ -271,13 +271,6 @@ double bottleneckDistExact(DiagramPointSet& A, DiagramPointSet& B)
                                             std::make_pair(ptB.getRealY() - delta, ptB),
                                             compLambda);
 
-            //if (ptB.id == 316) {
-                //std::cout << itStart - yCentersVec.begin() <<  " "  << distLInf(itStart->second, ptB) << std::endl;
-                //std::cout << "maxDist = " << maxDist << std::endl;
-                //std::cout << "minDist = " << minDist << std::endl;
-                //double pwDistDebug = distLInf(itStart->second, ptB);
-                //std::cout << ( pwDistDebug >= minDist and pwDistDebug <= maxDist) << std::endl;
-            //}
 
             for(auto iterA = itStart; iterA < yCentersVec.end(); ++iterA) {
                 if ( ptB.getRealY() < iterA->first - delta) {
@@ -286,19 +279,16 @@ double bottleneckDistExact(DiagramPointSet& A, DiagramPointSet& B)
                 double pwDist = distLInf(iterA->second, ptB);
                 //std::cout << 1000*minDist << " <= " << 1000*pwDist << " <= " << 1000*maxDist << std::endl;
                 if (pwDist >= minDist and pwDist <= maxDist) {
-                    //if (ptB.id == 316) {
-                        //std::cout << "adding " << pwDist << std::endl;
-                    //}
                     pairwiseDist.push_back(pwDist);
                 }
             }
         }
     }
 
-    //std::cerr << "pairwiseDist.size = " << pairwiseDist.size() << " out of " << A.size() * A.size() << std::endl;
+    //std::cout << "pairwiseDist.size = " << pairwiseDist.size() << " out of " << A.size() * A.size() << std::endl;
     std::sort(pairwiseDist.begin(), pairwiseDist.end());
     //for(auto ddd : pairwiseDist) {
-        //std::cerr << std::setprecision(15) << ddd << std::endl;
+        //std::cout << std::setprecision(15) << ddd << std::endl;
     //}
 
     return bottleneckDistExactFromSortedPwDist(A, B, pairwiseDist);
@@ -516,7 +506,9 @@ bool readDiagramPointSet(const char* fname, std::vector<std::pair<double, double
     result.clear();
     std::ifstream f(fname);
     if (!f.good()) {
+#ifndef FOR_R_TDA
         std::cerr << "Cannot open file " << fname << std::endl;
+#endif
         return false;
     }
     std::string line;
@@ -541,7 +533,9 @@ bool readDiagramPointSet(const char* fname, std::vector<std::pair<double, double
         double x, y;
         std::istringstream iss(line);
         if (not(iss >> x >> y)) {
+#ifndef FOR_R_TDA
             std::cerr << "Error in file " << fname << ", line number " << lineNumber << ": cannot parse \"" << line << "\"" << std::endl;
+#endif
             return false;
         }
         result.push_back(std::make_pair(x,y));
diff --git a/geom_bottleneck/bottleneck/src/bound_match.cpp b/geom_bottleneck/bottleneck/src/bound_match.cpp
index 06d3b67..a9ec93a 100644
--- a/geom_bottleneck/bottleneck/src/bound_match.cpp
+++ b/geom_bottleneck/bottleneck/src/bound_match.cpp
@@ -18,9 +18,12 @@ along with GeomBottleneck.  If not, see <http://www.gnu.org/licenses/>.
 
 */
 
-#include <iostream>
 #include <assert.h>
+#include "def_debug_bt.h"
 #include "bound_match.h"
+#ifndef FOR_R_TDA
+#include <iostream>
+#endif
 
 namespace geom_bt {
 /*static void printDebug(//bool isDebug, std::string s)*/
@@ -82,6 +85,7 @@ namespace geom_bt {
 //#endif
 /*}*/
 
+#ifndef FOR_R_TDA
 std::ostream& operator<<(std::ostream& output, const Matching& m)
 {
     output << "Matching: " << m.AToB.size() << " pairs (";
@@ -94,6 +98,7 @@ std::ostream& operator<<(std::ostream& output, const Matching& m)
     }
     return output;
 }
+#endif
 
 void Matching::sanityCheck() const
 {
@@ -103,8 +108,11 @@ void Matching::sanityCheck() const
         auto bToAPair = BToA.find(aToBPair.second);
         assert(bToAPair != BToA.end());
         if (aToBPair.first != bToAPair->second) {
+#ifndef FOR_R_TDA
             std::cerr << "failed assertion, in aToB " << aToBPair.first;
             std::cerr << ", in bToA " << bToAPair->second << std::endl;
+#endif
+            assert(false);
         }
         assert( aToBPair.first == bToAPair->second);
     }
@@ -151,7 +159,9 @@ void Matching::checkAugPath(const Path& augPath) const
     for(size_t idx = 0; idx < augPath.size(); ++idx) {
         bool mustBeExposed  { idx == 0 or idx == augPath.size() - 1 };
         if (isExposed(augPath[idx]) != mustBeExposed) {
+#ifndef FOR_R_TDA
             std::cerr << "mustBeExposed = " << mustBeExposed << ", idx = " << idx << ", point " << augPath[idx] << std::endl;
+#endif
         }
         assert( isExposed(augPath[idx]) == mustBeExposed );
         DiagramPoint matchedVertex {0.0, 0.0, DiagramPoint::DIAG, 1};
@@ -275,10 +285,12 @@ bool BoundMatchOracle::buildAugmentingPath(const DiagramPoint startVertex, Path&
                  // layer
                 DiagramPoint nextVertexA {0.0, 0.0, DiagramPoint::DIAG, 1};
                 if (!M.getMatchedVertex(nextVertexB, nextVertexA)) {
+#ifndef FOR_R_TDA
                     std::cerr << "Vertices in even layers must be matched! Unmatched: ";
                     std::cerr << nextVertexB << std::endl;
                     std::cerr << evenLayerIdx << "; " << layerGraph.size() << std::endl;
-                    throw "Unmatched vertex in even layer";
+#endif
+                    throw std::runtime_error("Unmatched vertex in even layer");
                 } else {
                     assert( ! (nextVertexA.getRealX() == 0 and nextVertexA.getRealY() == 0) );
                     result.push_back(nextVertexA);
@@ -383,8 +395,10 @@ bool BoundMatchOracle::buildMatchingForThreshold(const double r)
             } 
             if (augmentingPaths.empty()) {
                 //printDebug(isDebug,"augmenting paths must exist, but were not found!", M);
+#ifndef FOR_R_TDA
                 std::cerr << "augmenting paths must exist, but were not found!" << std::endl;
-                throw "bad epsilon?";
+#endif
+                throw std::runtime_error("bad epsilon?");
             }
             // swap all augmenting paths with matching to increase it
             //printDebug(isDebug,"before increase with augmenting paths:", M);
@@ -403,6 +417,7 @@ bool BoundMatchOracle::buildMatchingForThreshold(const double r)
 void BoundMatchOracle::printLayerGraph(void)
 {
 #ifdef DEBUG_BOUND_MATCH
+#ifndef FOR_R_TDA
     for(auto& layer : layerGraph) {
         std::cout << "{ ";
         for(auto& p : layer) {
@@ -411,6 +426,7 @@ void BoundMatchOracle::printLayerGraph(void)
         std::cout << "\b\b }" << std::endl;
     }
 #endif
+#endif
 }
 
 void BoundMatchOracle::buildLayerGraph(double r)
diff --git a/geom_bottleneck/bottleneck/src/neighb_oracle.cpp b/geom_bottleneck/bottleneck/src/neighb_oracle.cpp
index 40d043f..5005bc4 100644
--- a/geom_bottleneck/bottleneck/src/neighb_oracle.cpp
+++ b/geom_bottleneck/bottleneck/src/neighb_oracle.cpp
@@ -184,8 +184,10 @@ void NeighbOracleAnn::deletePoint(const DiagramPoint& p)
     diagonalPoints.erase(p, false);
     kdTree->delete_point(pointIdx);
 #ifdef DEBUG_NEIGHBOUR_ORACLE
+#ifndef FOR_R_TDA
     kdTree->Print(ANNtrue, std::cout);
 #endif
+#endif
 }
 
 bool NeighbOracleAnn::getNeighbour(const DiagramPoint& q, DiagramPoint& result) const