@@ -1,8 +1,8 @@

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 

-Version: 2.17.3

-Date: 2019-12-17

+Version: 2.17.4

+Date: 2019-12-19

 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),

 		     email = "rdiaz02@gmail.com"),

 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))

@@ -1,3 +1,6 @@

+Changes in version 2.17.4 (2019-12-19):

+	- fno-common: better way of dealing with verbose in magellan.

+

 Changes in version 2.17.3 (2019-12-17):

 	- Compiles with fno-common (for gcc 10).

@@ -14,7 +14,8 @@

 #define DEFAULT_FITNESS -99999999999

-extern char verbose;   /* if set to non-0 , become verbose */

+/* extern char verbose; */

+/* if set to non-0 , become verbose */

 /*

@@ -13,7 +13,7 @@

 #include "random.h"

 #include "summary_statistics.h"

 #include "models.h"

-

+#include "verbose.h"

@@ -95,7 +95,7 @@ int main( int argc, char ** argv ){

 	int i;

 	/* extern char verbose; */                  /* level of verbosity */

-	char verbose;    

+	/* char verbose;     */

 	int opt;

 	extern char *optarg;                /* external variables, see man 3 getopt */

@@ -11,6 +11,8 @@

 #include "calculus.h"

+#include "verbose.h"

+

 #define DATE "18 NOV 2013"

@@ -58,8 +60,9 @@ int main( int argc, char ** argv ){

 	char *outfile=NULL;

 	/* prevent confusion with the other extern verbose */

-	char verbose_fl_stats=0;

-

+	/* char verbose_fl_stats=0; */

+	verbose = 0;

+	

 	/*

 		Parse Input

 	*/

@@ -86,7 +89,8 @@ int main( int argc, char ** argv ){

 				break;

 			case 'v':

-				verbose_fl_stats=1;

+				/* verbose_fl_stats=1; */

+				verbose=1;				

 				break;

 			case 's':

@@ -116,7 +120,8 @@ int main( int argc, char ** argv ){

 	h = ReadFile( filename, opt_zero );

-	if(verbose_fl_stats)

+	/* if(verbose_fl_stats) */

+	if(verbose)	  

 		print_landscape( &h );

 	OutputSummaryStats( &h, FitnessRatio, opt_log, opt_short, "coco", outfile );

@@ -9,8 +9,7 @@

 #include "genotypes.h"

 #include "summary_statistics.h"

 #include "models.h"

-

-/* extern char verbose; */

+#include "verbose.h"

 /*

@@ -21,7 +20,7 @@

 */

 void HouseOfCards( struct landscape *l, float sigma){

-  char verbose;

+  /* extern char verbose; */

 	int i;

 	if( sigma <= 0 )

@@ -56,7 +55,7 @@ void HouseOfCards( struct landscape *l, float sigma){

 void Multiplicative( struct landscape *l , double s, double stdev, int  opt_single_fitness, float DimRet,  char opt_log )

 {

-  char verbose;

+  /* extern char verbose; */

 	int *genotype=NULL;

 	float *fa;  

@@ -167,7 +166,7 @@ void Multiplicative( struct landscape *l , double s, double stdev, int  opt_sing

 void Optimum( struct landscape *l , double mean_p, double sigma_p, double mean_o, double sigma_o )

 {

-  char verbose;

+  /* extern char verbose; */

 	int *genotype=NULL;

 	float *fa;  

@@ -268,7 +267,7 @@ void Optimum( struct landscape *l , double mean_p, double sigma_p, double mean_o

 void Kaufman_NK( struct landscape *l,  int K, short random ){

-	char verbose;

+	/* extern char verbose; */

 	int i,j, g;

@@ -428,7 +427,7 @@ void Kaufman_NK( struct landscape *l,  int K, short random ){

 */

 void Ising( struct landscape *l, float mu_c, float sigma_c, short opt_circ )

 {

-  char verbose;

+  /* extern char verbose; */

 	int i,g;

 	float *costs;

@@ -571,7 +570,7 @@ void MixedModel( struct landscape *fl, struct model_opt myoptions, int opt_log )

 	struct landscape fl_tmp;

-	char verbose;

+	/* extern char verbose; */

 	int g;

@@ -10,7 +10,7 @@

-extern char verbose;

+/* extern char verbose; */

new file mode 100644

@@ -0,0 +1,2 @@

+#include "verbose.h"

+char verbose = 0;

new file mode 100644

@@ -0,0 +1,6 @@

+#ifndef _VERBOSE_H_

+#define _VERBOSE_H_

+

+extern char verbose;

+

+#endif

@@ -35,7 +35,8 @@ MAGELLAN_SRC = FitnessLandscape/gamma.c\

         FitnessLandscape/summary_statistics.c\

         FitnessLandscape/epistasis_type.c\

         FitnessLandscape/decomposition.c\

-        FitnessLandscape/models.c

+        FitnessLandscape/models.c\

+	FitnessLandscape/verbose.c

 #        FitnessLandscape/common_drawings.c\ ## I do not use it and gives a warning

 MAGELLAN_OBJECTS = $(MAGELLAN_SRC:.c=.o)

@@ -1,15 +1,15 @@

 \usepackage[%

-		shash={a6c95a3},

-		lhash={a6c95a3f05c9d32bbdb27c5634bfc9d5dad7a776},

+		shash={e7b549e},

+		lhash={e7b549e2d6e2de8a97e3169a5622b598dcfa7250},

 		authname={ramon diaz-uriarte (at Phelsuma)},

 		authemail={rdiaz02@gmail.com},

-		authsdate={2019-12-17},

-		authidate={2019-12-17 13:12:29 +0100},

-		authudate={1576584749},

+		authsdate={2019-12-19},

+		authidate={2019-12-19 09:14:58 +0100},

+		authudate={1576743298},

 		commname={ramon diaz-uriarte (at Phelsuma)},

 		commemail={rdiaz02@gmail.com},

-		commsdate={2019-12-17},

-		commidate={2019-12-17 13:12:29 +0100},

-		commudate={1576584749},

-		refnames={ (HEAD -> master)}

+		commsdate={2019-12-19},

+		commidate={2019-12-19 09:14:58 +0100},

+		commudate={1576743298},

+		refnames={ (HEAD -> master, verbose)}

 	]{gitsetinfo}

\ No newline at end of file