New upstream version 8.2.12+dfsg (9174d35a) · Commits · Debian Med / raxml

README

+1 −1

Original line number	Diff line number	Diff line
		Standard RAxML version 8.2.11
		Standard RAxML version 8.2.12

		============================================================================================================

axml.c

+7 −2

Original line number	Diff line number	Diff line
		@@ -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

+3 −3

Original line number	Diff line number	Diff line
		@@ -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

multiple.c

+12 −12

Original line number	Diff line number	Diff line
		@@ -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

+16 −9

Original line number	Diff line number	Diff line
		@@ -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;
		}
		}

Makefile.SSE3.gcc

+1 −1

File changed.

Contains only whitespace changes.