gentoo-overlay/sci-biology/eugene/files/eugene-4.1d-Wformat.patch

Fix -Wformat warnings caused by wrong printf specifiers:
* Sensor.Riken.cc:95:61: warning: format ‘%d’ expects argument of type ‘int’, but
* argument 3 has type ‘std::vector<RAFLgene>::size_type {aka long unsigned int}’ [-Wformat=]
*    fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size());

--- a/src/Hits.cc
+++ b/src/Hits.cc
@@ -163,7 +163,7 @@
     if (ThisHit != NULL)
         for (int i=0; i<*NumHits-1; i++) ThisHit = ThisHit->Next;
 
-    while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
+    while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %ss\n", &deb, &fin,
                         &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
     {
         if (HSP) fprintf(stderr, "%s", HSP);
--- a/src/SensorPlugins/Est/Sensor.Est.cc
+++ b/src/SensorPlugins/Est/Sensor.Est.cc
@@ -1353,13 +1353,13 @@
     exit(2);
   }
 
-  fprintf(fp, "vPos %d\n",  vPos.size());
+  fprintf(fp, "vPos %zu\n",  vPos.size());
   for (int i=0; i< vPos.size();i++ )
   {
     fprintf(fp, "vPos %d\t%d\n",i,  vPos[i]);
   }
   
-  fprintf(fp, "vESTMatch %d\n",  vESTMatch.size());
+  fprintf(fp, "vESTMatch %zu\n",  vESTMatch.size());
   for (int i=0; i< vESTMatch.size();i++ )
   {
     fprintf(fp, "vESTMatch %d\t\n", vESTMatch[i]);
--- a/src/SensorPlugins/Riken/Sensor.Riken.cc
+++ b/src/SensorPlugins/Riken/Sensor.Riken.cc
@@ -92,7 +92,7 @@
   
   
   
-  fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size());
+  fprintf(stderr, "%zu RAFL EST pairs read, ", RAFLtmp.size());
   
   sort(RAFLtmp.begin(), RAFLtmp.end(), Before);
   
@@ -148,7 +148,7 @@
     }
   }
   
-  fprintf(stderr,"resulting %d\n",RAFL.size());
+  fprintf(stderr,"resulting %zu\n",RAFL.size());
   fflush(stderr);
 
   //    for (RAFLtmpindice=0; RAFLtmpindice< (int)RAFL.size(); RAFLtmpindice++) {
--- a/src/SensorPlugins/SMachine/Sensor.SMachine.cc
+++ b/src/SensorPlugins/SMachine/Sensor.SMachine.cc
@@ -197,7 +197,7 @@
   fclose(fp);
 
   if (end ==2) {
-    fprintf(stderr, "Error in SpliceMachine splice site file %s, line %d\n", name, len);
+    fprintf(stderr, "Error in SpliceMachine splice site file %s, line %zu\n", name, len);
     exit(2);
   }
 }
--- a/src/SoTerms.cc
+++ b/src/SoTerms.cc
@@ -67,14 +67,14 @@
     j++;
     if (line[0] == 'i' && line[1] == 'd') 
     {
-      i = sscanf(line, "id: %s", &value);
+      i = sscanf(line, "id: %s", value);
       if (i > 0) 
       {
 	char soId[60];
 	char soName[60];
 	strcpy (soId, value );
 	fgets (line, MAX_LINE, fp);
-	i = sscanf(line, "name: %s", &value);
+	i = sscanf(line, "name: %s", value);
 	strcpy (soName, value );
 	idToName_[to_string(soId)]=to_string(soName);
 	nameToId_[to_string(soName)]=to_string(soId);