path: root/buildfix.patch

diff -ruN RNAmicro1.1.4/Makefile RNAmicro1.1.4a/Makefile
--- RNAmicro1.1.4/Makefile	2014-08-07 09:00:31.000000000 +0200
+++ RNAmicro1.1.4a/Makefile	2015-09-19 13:32:15.872994369 +0200
@@ -1,7 +1,7 @@
 EXE	= RNAmicro
 CC	= gcc
 LL	= g++
-VERSION	= 1.0
+VERSION	= 1.1.4
 DISTNAME= RNAmicro
 WARN	= -Wall -pedantic 
 CCFLAGS	= -O1  -DUNUSED='' -g $(WARN)
@@ -15,11 +15,13 @@
 	  strand.c zscore.c descriptors.c
 OBJS    = $(foreach file, $(SRCS:.c=.o), $(file))
 all: $(EXE)
-$(EXE): $(OBJS)
+$(EXE): $(OBJS) svm.o
 	$(LL) $(CCFLAGS) $(LIBS) -o $(EXE) svm.o $(OBJS)
 $(OBJS): %.o: %.c
 	$(CC) -c $(CCFLAGS) $< -o $@
+svm.o:  svm.cpp svm.h
+	$(CC) -c $(CCFLAGS) svm.cpp -o svm.o
 veryclean:
 	rm -f $(OBJS) $(EXE)
 clean:
-	rm -f $(OBJS) core
+	rm -f $(OBJS) svm.o core
diff -ruN RNAmicro1.1.4/fold.c RNAmicro1.1.4a/fold.c
--- RNAmicro1.1.4/fold.c	2014-08-07 09:00:31.000000000 +0200
+++ RNAmicro1.1.4a/fold.c	2015-09-19 13:28:25.954382460 +0200
@@ -783,7 +783,7 @@
 
 /*---------------------------------------------------------------------------*/
 
-inline int HairpinE(int size, int type, int si1, int sj1, const char *string) {
+int HairpinE(int size, int type, int si1, int sj1, const char *string) {
   int energy;
   energy = (size <= 30) ? P->hairpin[size] :
     P->hairpin[30]+(int)(P->lxc*log((size)/30.));
@@ -811,7 +811,7 @@
 
 /*---------------------------------------------------------------------------*/
 
-inline PRIVATE int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2) {
+PRIVATE int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2) {
   /* compute energy of degree 2 loop (stack bulge or interior) */
   int n1, n2, m, energy;
   n1 = p-i-1;
@@ -853,7 +853,7 @@
 
 /*--------------------------------------------------------------------------*/
 
-inline int LoopEnergy(int n1, int n2, int type, int type_2,
+int LoopEnergy(int n1, int n2, int type, int type_2,
 		      int si1, int sj1, int sp1, int sq1) {
   /* compute energy of degree 2 loop (stack bulge or interior) */
   int nl, ns, energy;
diff -ruN RNAmicro1.1.4/svm.cpp RNAmicro1.1.4a/svm.cpp
--- RNAmicro1.1.4/svm.cpp	2014-08-07 09:03:56.000000000 +0200
+++ RNAmicro1.1.4a/svm.cpp	2015-09-19 13:26:10.468533764 +0200
@@ -5,8 +5,6 @@
 #include <float.h>
 #include <string.h>
 #include <stdarg.h>
-#include <limits.h>
-#include <locale.h>
 #include "svm.h"
 int libsvm_version = LIBSVM_VERSION;
 typedef float Qfloat;
@@ -74,7 +72,7 @@
 	// return some position p where [p,len) need to be filled
 	// (p >= len if nothing needs to be filled)
 	int get_data(const int index, Qfloat **data, int len);
-	void swap_index(int i, int j);
+	void swap_index(int i, int j);	
 private:
 	int l;
 	long int size;
@@ -194,7 +192,7 @@
 class QMatrix {
 public:
 	virtual Qfloat *get_Q(int column, int len) const = 0;
-	virtual double *get_QD() const = 0;
+	virtual Qfloat *get_QD() const = 0;
 	virtual void swap_index(int i, int j) const = 0;
 	virtual ~QMatrix() {}
 };
@@ -207,7 +205,7 @@
 	static double k_function(const svm_node *x, const svm_node *y,
 				 const svm_parameter& param);
 	virtual Qfloat *get_Q(int column, int len) const = 0;
-	virtual double *get_QD() const = 0;
+	virtual Qfloat *get_QD() const = 0;
 	virtual void swap_index(int i, int j) const	// no so const...
 	{
 		swap(x[i],x[j]);
@@ -414,7 +412,7 @@
 	char *alpha_status;	// LOWER_BOUND, UPPER_BOUND, FREE
 	double *alpha;
 	const QMatrix *Q;
-	const double *QD;
+	const Qfloat *QD;
 	double eps;
 	double Cp,Cn;
 	double *p;
@@ -444,7 +442,7 @@
 	virtual double calculate_rho();
 	virtual void do_shrinking();
 private:
-	bool be_shrunk(int i, double Gmax1, double Gmax2);
+	bool be_shrunk(int i, double Gmax1, double Gmax2);	
 };
 
 void Solver::swap_index(int i, int j)
@@ -476,7 +474,7 @@
 			nr_free++;
 
 	if(2*nr_free < active_size)
-		info("\nWARNING: using -h 0 may be faster\n");
+		info("\nWarning: using -h 0 may be faster\n");
 
 	if (nr_free*l > 2*active_size*(l-active_size))
 	{
@@ -558,10 +556,9 @@
 	// optimization step
 
 	int iter = 0;
-	int max_iter = max(10000000, l>INT_MAX/100 ? INT_MAX : 100*l);
 	int counter = min(l,1000)+1;
-	
-	while(iter < max_iter)
+
+	while(1)
 	{
 		// show progress and do shrinking
 
@@ -601,7 +598,7 @@
 
 		if(y[i]!=y[j])
 		{
-			double quad_coef = QD[i]+QD[j]+2*Q_i[j];
+			double quad_coef = Q_i[i]+Q_j[j]+2*Q_i[j];
 			if (quad_coef <= 0)
 				quad_coef = TAU;
 			double delta = (-G[i]-G[j])/quad_coef;
@@ -644,7 +641,7 @@
 		}
 		else
 		{
-			double quad_coef = QD[i]+QD[j]-2*Q_i[j];
+			double quad_coef = Q_i[i]+Q_j[j]-2*Q_i[j];
 			if (quad_coef <= 0)
 				quad_coef = TAU;
 			double delta = (G[i]-G[j])/quad_coef;
@@ -728,18 +725,6 @@
 		}
 	}
 
-	if(iter >= max_iter)
-	{
-		if(active_size < l)
-		{
-			// reconstruct the whole gradient to calculate objective value
-			reconstruct_gradient();
-			active_size = l;
-			info("*");
-		}
-		fprintf(stderr,"\nWARNING: reaching max number of iterations\n");
-	}
-
 	// calculate rho
 
 	si->rho = calculate_rho();
@@ -833,8 +818,8 @@
 					Gmax2 = G[j];
 				if (grad_diff > 0)
 				{
-					double obj_diff;
-					double quad_coef = QD[i]+QD[j]-2.0*y[i]*Q_i[j];
+					double obj_diff; 
+					double quad_coef=Q_i[i]+QD[j]-2.0*y[i]*Q_i[j];
 					if (quad_coef > 0)
 						obj_diff = -(grad_diff*grad_diff)/quad_coef;
 					else
@@ -857,8 +842,8 @@
 					Gmax2 = -G[j];
 				if (grad_diff > 0)
 				{
-					double obj_diff;
-					double quad_coef = QD[i]+QD[j]+2.0*y[i]*Q_i[j];
+					double obj_diff; 
+					double quad_coef=Q_i[i]+QD[j]+2.0*y[i]*Q_i[j];
 					if (quad_coef > 0)
 						obj_diff = -(grad_diff*grad_diff)/quad_coef;
 					else
@@ -1006,7 +991,7 @@
 //
 // additional constraint: e^T \alpha = constant
 //
-class Solver_NU: public Solver
+class Solver_NU : public Solver
 {
 public:
 	Solver_NU() {}
@@ -1085,8 +1070,8 @@
 					Gmaxp2 = G[j];
 				if (grad_diff > 0)
 				{
-					double obj_diff;
-					double quad_coef = QD[ip]+QD[j]-2*Q_ip[j];
+					double obj_diff; 
+					double quad_coef = Q_ip[ip]+QD[j]-2*Q_ip[j];
 					if (quad_coef > 0)
 						obj_diff = -(grad_diff*grad_diff)/quad_coef;
 					else
@@ -1109,8 +1094,8 @@
 					Gmaxn2 = -G[j];
 				if (grad_diff > 0)
 				{
-					double obj_diff;
-					double quad_coef = QD[in]+QD[j]-2*Q_in[j];
+					double obj_diff; 
+					double quad_coef = Q_in[in]+QD[j]-2*Q_in[j];
 					if (quad_coef > 0)
 						obj_diff = -(grad_diff*grad_diff)/quad_coef;
 					else
@@ -1271,9 +1256,9 @@
 	{
 		clone(y,y_,prob.l);
 		cache = new Cache(prob.l,(long int)(param.cache_size*(1<<20)));
-		QD = new double[prob.l];
+		QD = new Qfloat[prob.l];
 		for(int i=0;i<prob.l;i++)
-			QD[i] = (this->*kernel_function)(i,i);
+			QD[i]= (Qfloat)(this->*kernel_function)(i,i);
 	}
 	
 	Qfloat *get_Q(int i, int len) const
@@ -1288,7 +1273,7 @@
 		return data;
 	}
 
-	double *get_QD() const
+	Qfloat *get_QD() const
 	{
 		return QD;
 	}
@@ -1310,7 +1295,7 @@
 private:
 	schar *y;
 	Cache *cache;
-	double *QD;
+	Qfloat *QD;
 };
 
 class ONE_CLASS_Q: public Kernel
@@ -1320,9 +1305,9 @@
 	:Kernel(prob.l, prob.x, param)
 	{
 		cache = new Cache(prob.l,(long int)(param.cache_size*(1<<20)));
-		QD = new double[prob.l];
+		QD = new Qfloat[prob.l];
 		for(int i=0;i<prob.l;i++)
-			QD[i] = (this->*kernel_function)(i,i);
+			QD[i]= (Qfloat)(this->*kernel_function)(i,i);
 	}
 	
 	Qfloat *get_Q(int i, int len) const
@@ -1337,7 +1322,7 @@
 		return data;
 	}
 
-	double *get_QD() const
+	Qfloat *get_QD() const
 	{
 		return QD;
 	}
@@ -1356,7 +1341,7 @@
 	}
 private:
 	Cache *cache;
-	double *QD;
+	Qfloat *QD;
 };
 
 class SVR_Q: public Kernel
@@ -1367,7 +1352,7 @@
 	{
 		l = prob.l;
 		cache = new Cache(l,(long int)(param.cache_size*(1<<20)));
-		QD = new double[2*l];
+		QD = new Qfloat[2*l];
 		sign = new schar[2*l];
 		index = new int[2*l];
 		for(int k=0;k<l;k++)
@@ -1376,8 +1361,8 @@
 			sign[k+l] = -1;
 			index[k] = k;
 			index[k+l] = k;
-			QD[k] = (this->*kernel_function)(k,k);
-			QD[k+l] = QD[k];
+			QD[k]= (Qfloat)(this->*kernel_function)(k,k);
+			QD[k+l]=QD[k];
 		}
 		buffer[0] = new Qfloat[2*l];
 		buffer[1] = new Qfloat[2*l];
@@ -1410,7 +1395,7 @@
 		return buf;
 	}
 
-	double *get_QD() const
+	Qfloat *get_QD() const
 	{
 		return QD;
 	}
@@ -1431,7 +1416,7 @@
 	int *index;
 	mutable int next_buffer;
 	Qfloat *buffer[2];
-	double *QD;
+	Qfloat *QD;
 };
 
 //
@@ -1451,7 +1436,7 @@
 	{
 		alpha[i] = 0;
 		minus_ones[i] = -1;
-		if(prob->y[i] > 0) y[i] = +1; else y[i] = -1;
+		if(prob->y[i] > 0) y[i] = +1; else y[i]=-1;
 	}
 
 	Solver s;
@@ -1641,7 +1626,7 @@
 struct decision_function
 {
 	double *alpha;
-	double rho;
+	double rho;	
 };
 
 static decision_function svm_train_one(
@@ -1701,6 +1686,30 @@
 	return f;
 }
 
+//
+// svm_model
+// 
+struct svm_model
+{
+	struct svm_parameter param;	/* parameter */
+	int nr_class;		/* number of classes, = 2 in regression/one class svm */
+	int l;			/* total #SV */
+	struct svm_node **SV;		/* SVs (SV[l]) */
+	double **sv_coef;	/* coefficients for SVs in decision functions (sv_coef[k-1][l]) */
+	double *rho;		/* constants in decision functions (rho[k*(k-1)/2]) */
+	double *probA;		/* pariwise probability information */
+	double *probB;
+
+	/* for classification only */
+
+	int *label;		/* label of each class (label[k]) */
+	int *nSV;		/* number of SVs for each class (nSV[k]) */
+				/* nSV[0] + nSV[1] + ... + nSV[k-1] = l */
+	/* XXX */
+	int free_sv;		/* 1 if svm_model is created by svm_load_model*/
+				/* 0 if svm_model is created by svm_train */
+};
+
 // Platt's binary SVM Probablistic Output: an improvement from Lin et al.
 static void sigmoid_train(
 	int l, const double *dec_values, const double *labels, 
@@ -1722,7 +1731,7 @@
 	double *t=Malloc(double,l);
 	double fApB,p,q,h11,h22,h21,g1,g2,det,dA,dB,gd,stepsize;
 	double newA,newB,newf,d1,d2;
-	int iter;
+	int iter; 
 	
 	// Initial Point and Initial Fun Value
 	A=0.0; B=log((prior0+1.0)/(prior1+1.0));
@@ -1818,7 +1827,6 @@
 static double sigmoid_predict(double decision_value, double A, double B)
 {
 	double fApB = decision_value*A+B;
-	// 1-p used later; avoid catastrophic cancellation
 	if (fApB >= 0)
 		return exp(-fApB)/(1.0+exp(-fApB));
 	else
@@ -1961,11 +1969,11 @@
 			struct svm_model *submodel = svm_train(&subprob,&subparam);
 			for(j=begin;j<end;j++)
 			{
-				svm_predict_values(submodel,prob->x[perm[j]],&(dec_values[perm[j]]));
+				svm_predict_values(submodel,prob->x[perm[j]],&(dec_values[perm[j]])); 
 				// ensure +1 -1 order; reason not using CV subroutine
 				dec_values[perm[j]] *= submodel->label[0];
 			}		
-			svm_free_and_destroy_model(&submodel);
+			svm_destroy_model(submodel);
 			svm_destroy_param(&subparam);
 		}
 		free(subprob.x);
@@ -2018,7 +2026,7 @@
 	int nr_class = 0;
 	int *label = Malloc(int,max_nr_class);
 	int *count = Malloc(int,max_nr_class);
-	int *data_label = Malloc(int,l);
+	int *data_label = Malloc(int,l);	
 	int i;
 
 	for(i=0;i<l;i++)
@@ -2048,24 +2056,6 @@
 		}
 	}
 
-	//
-	// Labels are ordered by their first occurrence in the training set. 
-	// However, for two-class sets with -1/+1 labels and -1 appears first, 
-	// we swap labels to ensure that internally the binary SVM has positive data corresponding to the +1 instances.
-	//
-	if (nr_class == 2 && label[0] == -1 && label[1] == 1)
-	{
-		swap(label[0],label[1]);
-		swap(count[0],count[1]);
-		for(i=0;i<l;i++)
-		{
-			if(data_label[i] == 0)
-				data_label[i] = 1;
-			else
-				data_label[i] = 0;
-		}
-	}
-
 	int *start = Malloc(int,nr_class);
 	start[0] = 0;
 	for(i=1;i<nr_class;i++)
@@ -2125,14 +2115,12 @@
 		model->l = nSV;
 		model->SV = Malloc(svm_node *,nSV);
 		model->sv_coef[0] = Malloc(double,nSV);
-		model->sv_indices = Malloc(int,nSV);
 		int j = 0;
 		for(i=0;i<prob->l;i++)
 			if(fabs(f.alpha[i]) > 0)
 			{
 				model->SV[j] = prob->x[i];
 				model->sv_coef[0][j] = f.alpha[i];
-				model->sv_indices[j] = i+1;
 				++j;
 			}		
 
@@ -2149,10 +2137,7 @@
 		int *perm = Malloc(int,l);
 
 		// group training data of the same class
-		svm_group_classes(prob,&nr_class,&label,&start,&count,perm);
-		if(nr_class == 1) 
-			info("WARNING: training data in only one class. See README for details.\n");
-		
+		svm_group_classes(prob,&nr_class,&label,&start,&count,perm);		
 		svm_node **x = Malloc(svm_node *,l);
 		int i;
 		for(i=0;i<l;i++)
@@ -2170,7 +2155,7 @@
 				if(param->weight_label[i] == label[j])
 					break;
 			if(j == nr_class)
-				fprintf(stderr,"WARNING: class label %d specified in weight is not found\n", param->weight_label[i]);
+				fprintf(stderr,"warning: class label %d specified in weight is not found\n", param->weight_label[i]);
 			else
 				weighted_C[j] *= param->weight[i];
 		}
@@ -2274,14 +2259,9 @@
 
 		model->l = total_sv;
 		model->SV = Malloc(svm_node *,total_sv);
-		model->sv_indices = Malloc(int,total_sv);
 		p = 0;
 		for(i=0;i<l;i++)
-			if(nonzero[i])
-			{
-				model->SV[p] = x[i];
-				model->sv_indices[p++] = perm[i] + 1;
-			}
+			if(nonzero[i]) model->SV[p++] = x[i];
 
 		int *nz_start = Malloc(int,nr_class);
 		nz_start[0] = 0;
@@ -2339,16 +2319,11 @@
 void svm_cross_validation(const svm_problem *prob, const svm_parameter *param, int nr_fold, double *target)
 {
 	int i;
-	int *fold_start;
+	int *fold_start = Malloc(int,nr_fold+1);
 	int l = prob->l;
 	int *perm = Malloc(int,l);
 	int nr_class;
-	if (nr_fold > l)
-	{
-		nr_fold = l;
-		fprintf(stderr,"WARNING: # folds > # data. Will use # folds = # data instead (i.e., leave-one-out cross validation)\n");
-	}
-	fold_start = Malloc(int,nr_fold+1);
+
 	// stratified cv may not give leave-one-out rate
 	// Each class to l folds -> some folds may have zero elements
 	if((param->svm_type == C_SVC ||
@@ -2394,9 +2369,9 @@
 		fold_start[0]=0;
 		for (i=1;i<=nr_fold;i++)
 			fold_start[i] = fold_start[i-1]+fold_count[i-1];
-		free(start);
+		free(start);	
 		free(label);
-		free(count);
+		free(count);	
 		free(index);
 		free(fold_count);
 	}
@@ -2443,17 +2418,17 @@
 			double *prob_estimates=Malloc(double,svm_get_nr_class(submodel));
 			for(j=begin;j<end;j++)
 				target[perm[j]] = svm_predict_probability(submodel,prob->x[perm[j]],prob_estimates);
-			free(prob_estimates);
+			free(prob_estimates);			
 		}
 		else
 			for(j=begin;j<end;j++)
 				target[perm[j]] = svm_predict(submodel,prob->x[perm[j]]);
-		svm_free_and_destroy_model(&submodel);
+		svm_destroy_model(submodel);
 		free(subprob.x);
 		free(subprob.y);
 	}		
 	free(fold_start);
-	free(perm);
+	free(perm);	
 }
 
 
@@ -2474,18 +2449,6 @@
 			label[i] = model->label[i];
 }
 
-void svm_get_sv_indices(const svm_model *model, int* indices)
-{
-	if (model->sv_indices != NULL)
-		for(int i=0;i<model->l;i++)
-			indices[i] = model->sv_indices[i];
-}
-
-int svm_get_nr_sv(const svm_model *model)
-{
-	return model->l;
-}
-
 double svm_get_svr_probability(const svm_model *model)
 {
 	if ((model->param.svm_type == EPSILON_SVR || model->param.svm_type == NU_SVR) &&
@@ -2500,14 +2463,13 @@
 
 double svm_predict_values(const svm_model *model, const svm_node *x, double* dec_values)
 {
-	int i;
 	if(model->param.svm_type == ONE_CLASS ||
 	   model->param.svm_type == EPSILON_SVR ||
 	   model->param.svm_type == NU_SVR)
 	{
 		double *sv_coef = model->sv_coef[0];
 		double sum = 0;
-		for(i=0;i<model->l;i++)
+		for(int i=0;i<model->l;i++)
 			sum += sv_coef[i] * Kernel::k_function(x,model->SV[i],model->param);
 		sum -= model->rho[0];
 		*dec_values = sum;
@@ -2519,6 +2481,7 @@
 	}
 	else
 	{
+		int i;
 		int nr_class = model->nr_class;
 		int l = model->l;
 		
@@ -2621,7 +2584,7 @@
 		for(i=0;i<nr_class;i++)
 			free(pairwise_prob[i]);
 		free(dec_values);
-		free(pairwise_prob);
+		free(pairwise_prob);	     
 		return model->label[prob_max_idx];
 	}
 	else 
@@ -2643,9 +2606,6 @@
 	FILE *fp = fopen(model_file_name,"w");
 	if(fp==NULL) return -1;
 
-	char *old_locale = strdup(setlocale(LC_ALL, NULL));
-	setlocale(LC_ALL, "C");
-
 	const svm_parameter& param = model->param;
 
 	fprintf(fp,"svm_type %s\n", svm_type_table[param.svm_type]);
@@ -2724,10 +2684,6 @@
 			}
 		fprintf(fp, "\n");
 	}
-
-	setlocale(LC_ALL, old_locale);
-	free(old_locale);
-
 	if (ferror(fp) != 0 || fclose(fp) != 0) return -1;
 	else return 0;
 }
@@ -2753,25 +2709,29 @@
 	return line;
 }
 
-//
-// FSCANF helps to handle fscanf failures.
-// Its do-while block avoids the ambiguity when
-// if (...)
-//    FSCANF();
-// is used
-//
-#define FSCANF(_stream, _format, _var) do{ if (fscanf(_stream, _format, _var) != 1) return false; }while(0)
-bool read_model_header(FILE *fp, svm_model* model)
+svm_model *svm_load_model(const char *model_file_name)
 {
+	FILE *fp = fopen(model_file_name,"rb");
+	if(fp==NULL) return NULL;
+	
+	// read parameters
+
+	svm_model *model = Malloc(svm_model,1);
 	svm_parameter& param = model->param;
+	model->rho = NULL;
+	model->probA = NULL;
+	model->probB = NULL;
+	model->label = NULL;
+	model->nSV = NULL;
+
 	char cmd[81];
 	while(1)
 	{
-		FSCANF(fp,"%80s",cmd);
+		fscanf(fp,"%80s",cmd);
 
 		if(strcmp(cmd,"svm_type")==0)
 		{
-			FSCANF(fp,"%80s",cmd);
+			fscanf(fp,"%80s",cmd);
 			int i;
 			for(i=0;svm_type_table[i];i++)
 			{
@@ -2784,12 +2744,16 @@
 			if(svm_type_table[i] == NULL)
 			{
 				fprintf(stderr,"unknown svm type.\n");
-				return false;
+				free(model->rho);
+				free(model->label);
+				free(model->nSV);
+				free(model);
+				return NULL;
 			}
 		}
 		else if(strcmp(cmd,"kernel_type")==0)
 		{		
-			FSCANF(fp,"%80s",cmd);
+			fscanf(fp,"%80s",cmd);
 			int i;
 			for(i=0;kernel_type_table[i];i++)
 			{
@@ -2801,106 +2765,79 @@
 			}
 			if(kernel_type_table[i] == NULL)
 			{
-				fprintf(stderr,"unknown kernel function.\n");	
-				return false;
+				fprintf(stderr,"unknown kernel function.\n");
+				free(model->rho);
+				free(model->label);
+				free(model->nSV);
+				free(model);
+				return NULL;
 			}
 		}
 		else if(strcmp(cmd,"degree")==0)
-			FSCANF(fp,"%d",&param.degree);
+			fscanf(fp,"%d",&param.degree);
 		else if(strcmp(cmd,"gamma")==0)
-			FSCANF(fp,"%lf",&param.gamma);
+			fscanf(fp,"%lf",&param.gamma);
 		else if(strcmp(cmd,"coef0")==0)
-			FSCANF(fp,"%lf",&param.coef0);
+			fscanf(fp,"%lf",&param.coef0);
 		else if(strcmp(cmd,"nr_class")==0)
-			FSCANF(fp,"%d",&model->nr_class);
+			fscanf(fp,"%d",&model->nr_class);
 		else if(strcmp(cmd,"total_sv")==0)
-			FSCANF(fp,"%d",&model->l);
+			fscanf(fp,"%d",&model->l);
 		else if(strcmp(cmd,"rho")==0)
 		{
 			int n = model->nr_class * (model->nr_class-1)/2;
 			model->rho = Malloc(double,n);
 			for(int i=0;i<n;i++)
-				FSCANF(fp,"%lf",&model->rho[i]);
+				fscanf(fp,"%lf",&model->rho[i]);
 		}
 		else if(strcmp(cmd,"label")==0)
 		{
 			int n = model->nr_class;
 			model->label = Malloc(int,n);
 			for(int i=0;i<n;i++)
-				FSCANF(fp,"%d",&model->label[i]);
+				fscanf(fp,"%d",&model->label[i]);
 		}
 		else if(strcmp(cmd,"probA")==0)
 		{
 			int n = model->nr_class * (model->nr_class-1)/2;
 			model->probA = Malloc(double,n);
 			for(int i=0;i<n;i++)
-				FSCANF(fp,"%lf",&model->probA[i]);
+				fscanf(fp,"%lf",&model->probA[i]);
 		}
 		else if(strcmp(cmd,"probB")==0)
 		{
 			int n = model->nr_class * (model->nr_class-1)/2;
 			model->probB = Malloc(double,n);
 			for(int i=0;i<n;i++)
-				FSCANF(fp,"%lf",&model->probB[i]);
+				fscanf(fp,"%lf",&model->probB[i]);
 		}
 		else if(strcmp(cmd,"nr_sv")==0)
 		{
 			int n = model->nr_class;
 			model->nSV = Malloc(int,n);
 			for(int i=0;i<n;i++)
-				FSCANF(fp,"%d",&model->nSV[i]);
+				fscanf(fp,"%d",&model->nSV[i]);
 		}
 		else if(strcmp(cmd,"SV")==0)
 		{
 			while(1)
 			{
 				int c = getc(fp);
-				if(c==EOF || c=='\n') break;
+				if(c==EOF || c=='\n') break;	
 			}
 			break;
 		}
 		else
 		{
 			fprintf(stderr,"unknown text in model file: [%s]\n",cmd);
-			return false;
+			free(model->rho);
+			free(model->label);
+			free(model->nSV);
+			free(model);
+			return NULL;
 		}
 	}
 
-	return true;
-
-}
-
-svm_model *svm_load_model(const char *model_file_name)
-{
-	FILE *fp = fopen(model_file_name,"rb");
-	if(fp==NULL) return NULL;
-
-	char *old_locale = strdup(setlocale(LC_ALL, NULL));
-	setlocale(LC_ALL, "C");
-
-	// read parameters
-
-	svm_model *model = Malloc(svm_model,1);
-	model->rho = NULL;
-	model->probA = NULL;
-	model->probB = NULL;
-	model->sv_indices = NULL;
-	model->label = NULL;
-	model->nSV = NULL;
-	
-	// read header
-	if (!read_model_header(fp, model))
-	{
-		fprintf(stderr, "ERROR: fscanf failed to read model\n");
-		setlocale(LC_ALL, old_locale);
-		free(old_locale);
-		free(model->rho);
-		free(model->label);
-		free(model->nSV);
-		free(model);
-		return NULL;
-	}
-	
 	// read sv_coef and SV
 
 	int elements = 0;
@@ -2965,9 +2902,6 @@
 	}
 	free(line);
 
-	setlocale(LC_ALL, old_locale);
-	free(old_locale);
-
 	if (ferror(fp) != 0 || fclose(fp) != 0)
 		return NULL;
 
@@ -2975,49 +2909,20 @@
 	return model;
 }
 
-void svm_free_model_content(svm_model* model_ptr)
-{
-	if(model_ptr->free_sv && model_ptr->l > 0 && model_ptr->SV != NULL)
-		free((void *)(model_ptr->SV[0]));
-	if(model_ptr->sv_coef)
-	{
-		for(int i=0;i<model_ptr->nr_class-1;i++)
-			free(model_ptr->sv_coef[i]);
-	}
-
-	free(model_ptr->SV);
-	model_ptr->SV = NULL;
-
-	free(model_ptr->sv_coef);
-	model_ptr->sv_coef = NULL;
-
-	free(model_ptr->rho);
-	model_ptr->rho = NULL;
-
-	free(model_ptr->label);
-	model_ptr->label= NULL;
-
-	free(model_ptr->probA);
-	model_ptr->probA = NULL;
-
-	free(model_ptr->probB);
-	model_ptr->probB= NULL;
-
-	free(model_ptr->sv_indices);
-	model_ptr->sv_indices = NULL;
-
-	free(model_ptr->nSV);
-	model_ptr->nSV = NULL;
-}
-
-void svm_free_and_destroy_model(svm_model** model_ptr_ptr)
+void svm_destroy_model(svm_model* model)
 {
-	if(model_ptr_ptr != NULL && *model_ptr_ptr != NULL)
-	{
-		svm_free_model_content(*model_ptr_ptr);
-		free(*model_ptr_ptr);
-		*model_ptr_ptr = NULL;
-	}
+	if(model->free_sv && model->l > 0)
+		free((void *)(model->SV[0]));
+	for(int i=0;i<model->nr_class-1;i++)
+		free(model->sv_coef[i]);
+	free(model->SV);
+	free(model->sv_coef);
+	free(model->rho);
+	free(model->label);
+	free(model->probA);
+	free(model->probB);
+	free(model->nSV);
+	free(model);
 }
 
 void svm_destroy_param(svm_parameter* param)
diff -ruN RNAmicro1.1.4/svm.h RNAmicro1.1.4a/svm.h
--- RNAmicro1.1.4/svm.h	2014-08-07 09:00:31.000000000 +0200
+++ RNAmicro1.1.4a/svm.h	2015-09-19 13:26:06.338558698 +0200
@@ -1,10 +1,14 @@
 #ifndef _LIBSVM_H
 #define _LIBSVM_H
 
+#define LIBSVM_VERSION 291
+
 #ifdef __cplusplus
 extern "C" {
 #endif
 
+extern int libsvm_version;
+
 struct svm_node
 {
 	int index;
@@ -53,7 +57,7 @@
 void svm_get_labels(const struct svm_model *model, int *label);
 double svm_get_svr_probability(const struct svm_model *model);
 
-void svm_predict_values(const struct svm_model *model, const struct svm_node *x, double* dec_values);
+double svm_predict_values(const struct svm_model *model, const struct svm_node *x, double* dec_values);
 double svm_predict(const struct svm_model *model, const struct svm_node *x);
 double svm_predict_probability(const struct svm_model *model, const struct svm_node *x, double* prob_estimates);
 
@@ -63,6 +67,8 @@
 const char *svm_check_parameter(const struct svm_problem *prob, const struct svm_parameter *param);
 int svm_check_probability_model(const struct svm_model *model);
 
+void svm_set_print_string_function(void (*print_func)(const char *));
+
 #ifdef __cplusplus
 }
 #endif