@@ -28,6 +28,8 @@

 #include <Rmath.h>

+#include <R_ext/RConverters.h>

+

 #include <R_ext/Rdynload.h>

@@ -11,10 +11,6 @@

 #include "include/kmeans.h"

 #include "include/mtree.h"

-//R includes

-#include <R.h>

-#include <Rdefines.h>

-

 int argmin(vector& x, array<vector>& M)

 {

@@ -60,10 +56,9 @@ array<vector> kmeans_init(int K, matrix& X, double min_diff = 1e-10)

   if (i >= N)  // failure

     {

-      //std::cerr << "k-means: Unable to find k = " << K << " sufficiently (min_diff >= " << min_diff << ") different vectors!" << std::endl

-		//<< "         Try changing k or min_diff." << std::endl;

-      //exit(1);

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n k-means: Unable to find k = %d sufficiently (min_diff >= %5.3e) different vectors!\n Try changing k or min_diff.\n", K, min_diff);

+      std::cerr << "k-means: Unable to find k = " << K << " sufficiently (min_diff >= " << min_diff << ") different vectors!" << std::endl

+		<< "         Try changing k or min_diff." << std::endl;

+      exit(1);

     }

   return M;

@@ -11,10 +11,6 @@

 #include "include/mtree.h"

-//R includes

-#include <R.h>

-#include <Rdefines.h>

-

 array<string> load_profile(char *filestem, int L)

 {

@@ -44,9 +40,8 @@ array<string> load_profile(char *filestem, int L)

       if (j != L)

 	{

-	  //std::cerr << "Number of profile labels does not coincide with number of data columns and/or model dimensions!" << std::endl;

-	  //exit(1);

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n Number of profile labels does not coincide with number of data columns and/or model dimensions!\n see warnings() and restart R", 1);

+	  std::cerr << "Number of profile labels does not coincide with number of data columns and/or model dimensions!" << std::endl;

+	  exit(1);

 	}

     }

@@ -72,9 +67,8 @@ void save_profile(array<string>& profile, char* filestem)

   std::ofstream prf(filename);

   if (! prf)

     {

-      //std::cerr << "Can't open output file -- " << filename << std::endl;

-      //exit(1);

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n Can't open output file %s!\n see warnings() and restart R", 1, filename);

+      std::cerr << "Can't open output file -- " << filename << std::endl;

+      exit(1);

     }

   for (int j=0; j<L; j++)

@@ -96,9 +90,8 @@ integer_matrix load_pattern(char *filestem)

   std::ifstream patfile(filename);

   if (! patfile)

     {

-      //std::cerr << "Can't open input file -- " << filename << std::endl;

-      //exit(1);

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n Can't open input file %s!\n see warnings() and restart R", 1, filename);

+      std::cerr << "Can't open input file -- " << filename << std::endl;

+      exit(1);

     }

   patfile >> pattern;

   patfile.close();

@@ -116,9 +109,8 @@ void save_pattern(integer_matrix& pattern, char *filestem)

   std::ofstream patfile(filename);

   if (! patfile)

     {

-      //std::cerr << "Can't open output file -- " << filename << std::endl;

-      //exit(1);

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n Can't open output file %s!\n see warnings() and restart R", 1, filename);

+      std::cerr << "Can't open output file -- " << filename << std::endl;

+      exit(1);

     }

   patfile << pattern;

   patfile.close();

@@ -155,8 +147,7 @@ matrix pair_probs(integer_matrix& pat, vector& resp)

 	if (count == 0)  // no data in the column pair (j1,j2)

 	  {

-	    //std::cerr << "Warning: No data in column pair (" << j1 << ", " << j2 << ")! Assuming independence." << std::endl;

-		Rprintf("Warning: No data in column pair (%d, %d)! Assuming independence!\n", j1, j2);

+	    std::cerr << "Warning: No data in column pair (" << j1 << ", " << j2 << ")! Assuming independence." << std::endl;

 	    wcount = P(0,j1) * P(0,j2);  // assuming independence

 	  }

@@ -10,9 +10,6 @@

 #include "include/mtree.h"

 #include "include/mtreemix.h"

-//R includes

-#include <R.h>

-#include <Rdefines.h>

 vector event_freq(integer_matrix& pat)

 {

@@ -27,9 +24,8 @@ vector event_freq(integer_matrix& pat)

       freq[j] = nonnegmean(col);  // == rel. frequency

       if (freq[j] < 0.0)  // no data in this column!

 	{

-	  //std::cerr << "No data in column " << j << " !" << std::endl;

-	  //exit(1);	

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n No data in column %2d!\n see warnings() and restart R", 1, j);

+	  std::cerr << "No data in column " << j << " !" << std::endl;

+	  exit(1);

 	}

     }

@@ -464,12 +460,11 @@ double mtreemix_EM(array<string>& profile, integer_matrix& pattern, int K, int M

 	  double sum = oneK * wlike.row(i);  // sum of weighted likelihoods

 	  if (sum <= 0.0)

 	    {

-	      //std::cerr << "EM aborted. Sample no. " << i + 1

-			//<< " [" << pat_hat.row(i) << "] "

-			//<< "has likelihood zero!" << std::endl;

+	      std::cerr << "EM aborted. Sample no. " << i + 1

+			<< " [" << pat_hat.row(i) << "] "

+			<< "has likelihood zero!" << std::endl;

 	      // mtreemix_save(alpha, G, cond_prob, node_no, "Lzero");  // save model for diagnostics

-	      //exit(1);

-		  Rf_error("internal: mtreemix invoked 'exit(%d)'\n EM aborted. Sample no. %2d has likelihood zero!\n see warnings() and restart R", 1, i + 1);

+	      exit(1);

 	    }

 	  for (int k=0; k<K; k++)

@@ -594,12 +589,11 @@ double mtreemix_E_step(integer_matrix& pattern, int K, vector& alpha, array< gra

 	  double sum = oneK * wlike.row(i);  // sum of weighted likelihoods

 	  if (sum <= 0.0)

 	    {

-	      //std::cerr << "E-step aborted. Sample no. " << i + 1

-			//<< " [" << pat_hat.row(i) << "] "

-		//	<< "has likelihood zero!" << std::endl;

+	      std::cerr << "E-step aborted. Sample no. " << i + 1

+			<< " [" << pat_hat.row(i) << "] "

+			<< "has likelihood zero!" << std::endl;

 	      // mtreemix_save(alpha, G, cond_prob, node_no, "Lzero");  // save model for diagnostics

-	      //exit(1);

-		  Rf_error("internal: mtreemix invoked 'exit(%d)'\n EM aborted. Sample no. %2d has likelihood zero!\n see warnings() and restart R", 1, i + 1);

+	      exit(1);

 	    }

 	  for (int k=0; k<K; k++)

@@ -629,8 +623,7 @@ double mtreemix_loglike(integer_matrix& pattern, int K, vector& alpha, array<gra

       if (sum <= 0.0)

 	{

-	  //std::cerr << "Warning: The sample: [" << pattern.row(i) << "] has likelihood zero!" << std::endl;

-	  Rprintf("Warning: Sample no. %2d has likelihood zero!", i);

+	  std::cerr << "Warning: The sample: [" << pattern.row(i) << "] has likelihood zero!" << std::endl;

 	}

       logL += log(sum);

@@ -740,9 +733,8 @@ void mtreemix_save(vector& alpha, array< graph >& G, array< map<edge,double> >&

   std::ofstream mtreemix(filename);

   if (! mtreemix)

     {

-      //std::cerr << "Can't open output file -- " << filename << std::endl;

-      //exit(1);

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n Can't open output file %s!\n see warnings() and restart R", 1, filename);

+      std::cerr << "Can't open output file -- " << filename << std::endl;

+      exit(1);

     }

   mtreemix << alpha << std::endl;

@@ -774,9 +766,8 @@ array<string> mtreemix_load(vector& alpha, array< graph >& G, array< map<node,st

   std::ifstream mtreemix(filename);

   if (! mtreemix)

     {

-      //std::cerr << "Can't open input file -- " << filename << std::endl;

-      //exit(1);

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n Can't open input file %s!\n see warnings() and restart R", 1, filename);

+      std::cerr << "Can't open input file -- " << filename << std::endl;

+      exit(1);

     }

   mtreemix >> alpha >> std::ws;

@@ -889,9 +880,8 @@ array< map<edge,double> > waiting_times(array< map<edge,double> >& cond_prob, in

       break;

     default :

-      //std::cerr << "Unknown sampling_mode -- " << sampling_mode << std::endl;

-      //exit(1);

-	  Rf_error("internal: mtreemix invoked 'exit(%d)'\n Unknown sampling mode %2d!\n see warnings() and restart R", 1, sampling_mode);

+      std::cerr << "Unknown sampling_mode -- " << sampling_mode << std::endl;

+      exit(1);

     }

   return lambda;

 }

@@ -4,10 +4,6 @@

 #include <cstdarg>

 #include <sstream>

-//R includes

-#include <R.h>

-#include <Rdefines.h>

-

 //using namespace replaceleda;

 //template<class T>

@@ -368,10 +364,9 @@ void replaceleda::printGraph (replaceleda::graph &g, edge_array<double> &weights

    node v;

     edge e;

-    //std::cerr << "#nodes: " << g.number_of_nodes() << " #edges: " << g.number_of_edges() << std::endl;

-	Rprintf("#nodes %2d #edges %2d\n", g.number_of_nodes(), g.number_of_edges());

+    std::cerr << "#nodes: " << g.number_of_nodes() << " #edges: " << g.number_of_edges() << std::endl;

     list<node> xxx = g.all_nodes();

-    /*

+    

     forall_nodes(v, g){

 	std::cerr << v << " " << v->getIndex() << std::endl;

 	std::cerr << "(" << g.indeg(v) << "," << g.outdeg(v) << "," << g.degree(v) << "):" << std::endl;

@@ -381,7 +376,7 @@ void replaceleda::printGraph (replaceleda::graph &g, edge_array<double> &weights

 	    std::cerr << v->getIndex() << " -" << weights[e] << "-> " << t->getIndex() << std::endl; 

 	}

     }

-	*/

+

 }