README

-Standard RAxML version 8.2.11
+Standard RAxML version 8.2.12
 
 ============================================================================================================
 

axml.c

@@ -6601,11 +6601,16 @@ static void get_args(int argc, char *argv[], analdef *adef, tree *tr)
 	{
 	  printf("All options supported\n");
 	  fprintf(flagCheckFile, "All options supported\n");
-	}
-     
 	  fclose(flagCheckFile);
 	  exit(0);
 	}
+      else
+	{
+	  fclose(flagCheckFile);
+	  exit(-1);
+	}
+     
+    }
   
   if(tr->useAccumulatedEPACutoff && epaSet)
     {

axml.h

@@ -168,9 +168,9 @@
 #define PointGamma(prob,alpha,beta)  PointChi2(prob,2.0*(alpha))/(2.0*(beta))
 
 #define programName        "RAxML"
-#define programVersion     "8.2.11"
-#define programVersionInt   8211
-#define programDate        "June 2017"
+#define programVersion     "8.2.12"
+#define programVersionInt   8212
+#define programDate        "May 2018"
 
 
 #define  TREE_EVALUATION                 0

debian/changelog

+raxml (8.2.12+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Fri, 08 Jun 2018 10:58:27 +0200
+
 raxml (8.2.11+dfsg-1) unstable; urgency=medium
 
   [ Shamika Mohanan ]

debian/compat

-10
+11

debian/control

@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                help2man
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/raxml.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/raxml.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/raxml
+Vcs-Git: https://salsa.debian.org/med-team/raxml.git
 Homepage: http://www.exelixis-lab.org/
 
 Package: raxml

multiple.c

@@ -831,15 +831,15 @@ void doAllInOne(tree *tr, analdef *adef)
 		break;
 	      case MR_STOP:
 		printBothOpenMPI("Stopped Rapid BS search after %d replicates with MR-based Bootstopping criterion\n", bootstrapsPerformed);
-		printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);	     
+		printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);	     
 		break;
 	      case MRE_STOP:
 		printBothOpenMPI("Stopped Rapid BS search after %d replicates with MRE-based Bootstopping criterion\n", bootstrapsPerformed);
-		printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);	     
+		printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);	     
 		break;
 	      case MRE_IGN_STOP:
 		printBothOpenMPI("Stopped Rapid BS search after %d replicates with MRE_IGN-based Bootstopping criterion\n", bootstrapsPerformed);
-		printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);	     
+		printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);	     
 		break;
 	      default:
 		assert(0);
@@ -855,15 +855,15 @@ void doAllInOne(tree *tr, analdef *adef)
 		break;
 	      case MR_STOP:
 		printBothOpenMPI("Rapid BS search did not converge after %d replicates with MR-based Bootstopping criterion\n", bootstrapsPerformed);
-		printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
+		printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
 		break;
 	      case MRE_STOP:
 		printBothOpenMPI("Rapid BS search did not converge after %d replicates with MRE-based Bootstopping criterion\n", bootstrapsPerformed);
-		printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
+		printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
 		break;
 	      case MRE_IGN_STOP:
 		printBothOpenMPI("Rapid BS search did not converge after %d replicates with MR_IGN-based Bootstopping criterion\n", bootstrapsPerformed);
-		printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
+		printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
 		break;
 	      default:
 		assert(0);
@@ -1348,15 +1348,15 @@ void doBootstrap(tree *tr, analdef *adef, rawdata *rdta, cruncheddata *cdta)
 	      break;
 	    case MR_STOP:
 	      printBothOpenMPI("Stopped Standard BS search after %d replicates with MR-based Bootstopping criterion\n", bootstrapsPerformed);
-	      printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);	     
+	      printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);	     
 	      break;
 	    case MRE_STOP:
 	      printBothOpenMPI("Stopped Standard BS search after %d replicates with MRE-based Bootstopping criterion\n", bootstrapsPerformed);
-	      printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);	     
+	      printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);	     
 	      break;
 	    case MRE_IGN_STOP:
 	      printBothOpenMPI("Stopped Standard BS search after %d replicates with MRE_IGN-based Bootstopping criterion\n", bootstrapsPerformed);
-	      printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);	     
+	      printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);	     
 	      break;
 	    default:
 	      assert(0);
@@ -1372,15 +1372,15 @@ void doBootstrap(tree *tr, analdef *adef, rawdata *rdta, cruncheddata *cdta)
 	      break;
 	    case MR_STOP:
 	      printBothOpenMPI("Standard BS search did not converge after %d replicates with MR-based Bootstopping criterion\n", bootstrapsPerformed);
-	      printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
+	      printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
 	      break;
 	    case MRE_STOP:
 	      printBothOpenMPI("Standard BS search did not converge after %d replicates with MRE-based Bootstopping criterion\n", bootstrapsPerformed);
-	      printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
+	      printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
 	      break;
 	    case MRE_IGN_STOP:
 	      printBothOpenMPI("Standard BS search did not converge after %d replicates with MR_IGN-based Bootstopping criterion\n", bootstrapsPerformed);
-	      printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
+	      printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
 	      break;
 	    default:
 	      assert(0);

parsePartitions.c

@@ -642,7 +642,16 @@ static int myGetline(char **lineptr, int *n, FILE *stream)
   return p - *lineptr;
 }
 
-
+static void nonContiguousError(analdef *adef)
+{
+  if(adef->compressPatterns == FALSE)
+    {
+      printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n");
+      printf("to the same partition model, when pattern compression is disabled via the -H flag,\n");
+      printf("or when pattern compression is disabled implicitely by some other option that requires it!\n\n");
+      exit(-1);
+    }
+}
 
 void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
 {
@@ -775,6 +784,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
       if(*ch == ',')
 	{	     
 	  upper = lower;
+	  nonContiguousError(adef);
 	  goto SINGLE_NUMBER;
 	}
       
@@ -818,6 +828,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
       if(*ch == ',')
 	{	 
 	  ch++;
+	  nonContiguousError(adef);
 	  goto numberPairs;
 	}
       
@@ -832,13 +843,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
 	      exit(-1);
 	    }     
 
-	   if(adef->compressPatterns == FALSE)
-	    {
-	      printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n");
-	      printf("to the same partition model, when pattern compression is disabled via the -H flag,\n");
-	      printf("or when pattern compression is disabled implicitely by some other option that requires it!\n\n");
-	      exit(-1);
-	    }
+	  nonContiguousError(adef);
 	  
 	  l = 0;
 	  while(isNum(*ch))
@@ -856,9 +861,11 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
 	    {	     
 	      goto parsed;
 	    }
+
 	  if(*ch == ',')
 	    {	       
 	      ch++;
+	      nonContiguousError(adef);
 	      goto numberPairs;
 	    }
 	}