[med-svn] [Git][med-team/raxml][master] 8 commits: New upstream version 8.2.11+dfsg
Andreas Tille
gitlab at salsa.debian.org
Fri Jun 8 10:01:31 BST 2018
Andreas Tille pushed to branch master at Debian Med / raxml
Commits:
6732e011 by Andreas Tille at 2017-11-07T14:46:15+01:00
New upstream version 8.2.11+dfsg
- - - - -
9174d35a by Andreas Tille at 2018-06-08T10:58:17+02:00
New upstream version 8.2.12+dfsg
- - - - -
8521ec46 by Andreas Tille at 2018-06-08T10:58:18+02:00
Update upstream source from tag 'upstream/8.2.12+dfsg'
Update to upstream version '8.2.12+dfsg'
with Debian dir 43d206dbeb39a7e68231b7a5e1c744078cf9e52f
- - - - -
e690210b by Andreas Tille at 2018-06-08T10:58:18+02:00
New upstream version
- - - - -
c87039f9 by Andreas Tille at 2018-06-08T10:58:19+02:00
debhelper 11
- - - - -
5d0b563d by Andreas Tille at 2018-06-08T10:58:26+02:00
Point Vcs fields to salsa.debian.org
- - - - -
3d0af604 by Andreas Tille at 2018-06-08T10:58:26+02:00
Standards-Version: 4.1.4
- - - - -
298b9413 by Andreas Tille at 2018-06-08T11:00:39+02:00
Upload to unstable
- - - - -
9 changed files:
- Makefile.SSE3.gcc
- README
- axml.c
- axml.h
- debian/changelog
- debian/compat
- debian/control
- multiple.c
- parsePartitions.c
Changes:
=====================================
Makefile.SSE3.gcc
=====================================
--- a/Makefile.SSE3.gcc
+++ b/Makefile.SSE3.gcc
@@ -3,7 +3,7 @@
CC = gcc
-CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops #-pedantic -Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops #-pedantic -Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
LIBRARIES = -lm
=====================================
README
=====================================
--- a/README
+++ b/README
@@ -1,4 +1,4 @@
-Standard RAxML version 8.2.11
+Standard RAxML version 8.2.12
============================================================================================================
=====================================
axml.c
=====================================
--- a/axml.c
+++ b/axml.c
@@ -6601,10 +6601,15 @@ 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);
}
- fclose(flagCheckFile);
- exit(0);
}
if(tr->useAccumulatedEPACutoff && epaSet)
=====================================
axml.h
=====================================
--- a/axml.h
+++ b/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
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+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 at debian.org> Fri, 08 Jun 2018 10:58:27 +0200
+
raxml (8.2.11+dfsg-1) unstable; urgency=medium
[ Shamika Mohanan ]
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at 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
=====================================
--- a/multiple.c
+++ b/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
=====================================
--- a/parsePartitions.c
+++ b/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;
}
@@ -831,15 +842,9 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
printf("%c Number expected in %s\n", *ch, p_names[i]);
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;
}
}
View it on GitLab: https://salsa.debian.org/med-team/raxml/compare/992a5bcfe9260ee3ff784105433ad5280ac0a01a...298b94130831b129bf0cf6f5579581db7b8bcf52
--
View it on GitLab: https://salsa.debian.org/med-team/raxml/compare/992a5bcfe9260ee3ff784105433ad5280ac0a01a...298b94130831b129bf0cf6f5579581db7b8bcf52
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