6 files changed, 40 insertions, 5 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