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###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL muscle
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘muscle’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c aligngivenpath.cpp -o aligngivenpath.o
aligngivenpath.cpp: In function ‘void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)’:
aligngivenpath.cpp:186:17: warning: unused variable ‘uLengthA’ [-Wunused-variable]
const unsigned uLengthA = msaA.GetColCount();
^~~~~~~~
aligngivenpath.cpp:187:17: warning: unused variable ‘uLengthB’ [-Wunused-variable]
const unsigned uLengthB = msaB.GetColCount();
^~~~~~~~
aligngivenpath.cpp: In function ‘void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpath.cpp:335:19: warning: unused variable ‘uColA’ [-Wunused-variable]
const unsigned uColA = uPrefixLengthA - 1;
^~~~~
aligngivenpath.cpp:336:19: warning: unused variable ‘uColB’ [-Wunused-variable]
const unsigned uColB = uPrefixLengthB - 1;
^~~~~
aligngivenpath.cpp:346:19: warning: unused variable ‘uColA’ [-Wunused-variable]
const unsigned uColA = uPrefixLengthA - 1;
^~~~~
aligngivenpath.cpp:354:19: warning: unused variable ‘uColB’ [-Wunused-variable]
const unsigned uColB = uPrefixLengthB - 1;
^~~~~
In file included from muscle.h:34:0,
from aligngivenpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c aligngivenpathsw.cpp -o aligngivenpathsw.o
aligngivenpathsw.cpp: In function ‘void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)’:
aligngivenpathsw.cpp:58:17: warning: unused variable ‘uLengthA’ [-Wunused-variable]
const unsigned uLengthA = msaA.GetColCount();
^~~~~~~~
aligngivenpathsw.cpp:59:17: warning: unused variable ‘uLengthB’ [-Wunused-variable]
const unsigned uLengthB = msaB.GetColCount();
^~~~~~~~
aligngivenpathsw.cpp: In function ‘void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpathsw.cpp:204:19: warning: unused variable ‘uColA’ [-Wunused-variable]
const unsigned uColA = uPrefixLengthA - 1;
^~~~~
aligngivenpathsw.cpp:205:19: warning: unused variable ‘uColB’ [-Wunused-variable]
const unsigned uColB = uPrefixLengthB - 1;
^~~~~
aligngivenpathsw.cpp:215:19: warning: unused variable ‘uColA’ [-Wunused-variable]
const unsigned uColA = uPrefixLengthA - 1;
^~~~~
aligngivenpathsw.cpp:223:19: warning: unused variable ‘uColB’ [-Wunused-variable]
const unsigned uColB = uPrefixLengthB - 1;
^~~~~
In file included from muscle.h:34:0,
from aligngivenpathsw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c aligntwomsas.cpp -o aligntwomsas.o
In file included from muscle.h:34:0,
from aligntwomsas.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c aligntwoprofs.cpp -o aligntwoprofs.o
In file included from muscle.h:34:0,
from aligntwoprofs.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c aln.cpp -o aln.o
In file included from muscle.h:34:0,
from aln.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c alpha.cpp -o alpha.o
alpha.cpp: In function ‘unsigned int GetAlphaSize(ALPHA)’:
alpha.cpp:84:9: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch]
switch (Alpha)
^
In file included from muscle.h:34:0,
from alpha.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c anchors.cpp -o anchors.o
anchors.cpp: In function ‘void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)’:
anchors.cpp:162:13: warning: unused variable ‘uWindowCenter’ [-Wunused-variable]
unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
^~~~~~~~~~~~~
anchors.cpp: At global scope:
anchors.cpp:105:13: warning: ‘void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)’ defined but not used [-Wunused-function]
static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
^~~~~~~~~~~~
anchors.cpp:53:13: warning: ‘void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)’ defined but not used [-Wunused-function]
static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
^~~~~~~~~~~~~~~~~
In file included from muscle.h:34:0,
from anchors.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function ‘void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)’:
bittraceback.cpp:146:7: warning: unused variable ‘Bits’ [-Wunused-variable]
char Bits = TraceBack[uLengthA][uLengthB];
^~~~
bittraceback.cpp: At global scope:
bittraceback.cpp:15:20: warning: ‘const char* BitsToStr(char)’ defined but not used [-Wunused-function]
static const char *BitsToStr(char Bits)
^~~~~~~~~
In file included from muscle.h:34:0,
from bittraceback.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c blosum62.cpp -o blosum62.o
In file included from muscle.h:34:0,
from blosum62.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c blosumla.cpp -o blosumla.o
blosumla.cpp:7:14: warning: ‘Blosum62LA’ defined but not used [-Wunused-variable]
static float Blosum62LA[20][20] =
^~~~~~~~~~
In file included from muscle.h:34:0,
from blosumla.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c clust.cpp -o clust.o
clust.cpp: In member function ‘void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:167:9: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch]
switch (m_JoinStyle)
^
clust.cpp: In member function ‘void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:184:17: warning: unused variable ‘uClusterCount’ [-Wunused-variable]
const unsigned uClusterCount = GetClusterCount();
^~~~~~~~~~~~~
clust.cpp: In member function ‘void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:204:17: warning: unused variable ‘uClusterCount’ [-Wunused-variable]
const unsigned uClusterCount = GetClusterCount();
^~~~~~~~~~~~~
clust.cpp: In member function ‘float Clust::ComputeDist(unsigned int, unsigned int)’:
clust.cpp:295:9: warning: enumeration value ‘LINKAGE_Undefined’ not handled in switch [-Wswitch]
switch (m_CentroidStyle)
^
clust.cpp: In member function ‘float Clust::ComputeDistMAFFT(unsigned int, unsigned int)’:
clust.cpp:360:14: warning: unused variable ‘dDistLR’ [-Wunused-variable]
const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
^~~~~~~
clust.cpp: In member function ‘float Clust::ComputeMetric(unsigned int, unsigned int) const’:
clust.cpp:611:9: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch]
switch (m_JoinStyle)
^
In file included from muscle.h:34:0,
from clust.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cluster.cpp -o cluster.o
cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’:
cluster.cpp:284:8: warning: variable ‘bFound’ set but not used [-Wunused-but-set-variable]
bool bFound = false;
^~~~~~
cluster.cpp:267:9: warning: unused variable ‘dMaxDist’ [-Wunused-variable]
double dMaxDist = 0.0;
^~~~~~~~
In file included from muscle.h:34:0,
from cluster.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’:
cluster.cpp:331:65: warning: ‘uIndexClosest2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
float dDist2 = ClusterDist.GetDist(uNodeIndex, uIndexClosest2);
^
cluster.cpp:307:47: warning: ‘uIndexClosest1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterNode &Child1 = m_Nodes[uIndexClosest1];
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c clwwt.cpp -o clwwt.o
In file included from muscle.h:34:0,
from clwwt.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c color.cpp -o color.o
color.cpp:72:12: warning: ‘int BlosumScore(char, char)’ defined but not used [-Wunused-function]
static int BlosumScore(char c1, char c2)
^~~~~~~~~~~
In file included from muscle.h:34:0,
from color.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cons.cpp -o cons.o
In file included from muscle.h:34:0,
from cons.cpp:7:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c diaglist.cpp -o diaglist.o
In file included from muscle.h:34:0,
from diaglist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
diaglist.cpp: In member function ‘void DiagList::FromPath(const PWPath&)’:
diaglist.cpp:77:6: warning: ‘uStartPosB’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Add(uStartPosA, uStartPosB, uLength);
~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diaglist.cpp:77:6: warning: ‘uStartPosA’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function ‘SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)’:
diffobjscore.cpp:76:17: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
const unsigned uSeqCount = msa.GetSeqCount();
^~~~~~~~~
diffobjscore.cpp:77:17: warning: unused variable ‘uColCount’ [-Wunused-variable]
const unsigned uColCount = msa.GetColCount();
^~~~~~~~~
In file included from muscle.h:34:0,
from diffobjscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c diffpaths.cpp -o diffpaths.o
In file included from muscle.h:34:0,
from diffpaths.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function ‘void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)’:
difftrees.cpp:161:17: warning: unused variable ‘uLeafCount2’ [-Wunused-variable]
const unsigned uLeafCount2 = Tree2.GetLeafCount();
^~~~~~~~~~~
In file included from muscle.h:34:0,
from difftrees.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c difftreese.cpp -o difftreese.o
In file included from muscle.h:34:0,
from difftreese.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c distcalc.cpp -o distcalc.o
In file included from muscle.h:34:0,
from distcalc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c distfunc.cpp -o distfunc.o
In file included from muscle.h:34:0,
from distfunc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c distpwkimura.cpp -o distpwkimura.o
In file included from muscle.h:34:0,
from distpwkimura.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c domuscle.cpp -o domuscle.o
In file included from muscle.h:34:0,
from domuscle.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dosp.cpp -o dosp.o
In file included from muscle.h:34:0,
from dosp.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function ‘void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)’:
dpreglist.cpp:82:19: warning: unused variable ‘uDiagLengthMinusCaps’ [-Wunused-variable]
const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
^~~~~~~~~~~~~~~~~~~~
In file included from muscle.h:34:0,
from dpreglist.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c drawtree.cpp -o drawtree.o
In file included from muscle.h:34:0,
from drawtree.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c edgelist.cpp -o edgelist.o
In file included from muscle.h:34:0,
from edgelist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c enumopts.cpp -o enumopts.o
In file included from muscle.h:34:0,
from enumopts.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c enumtostr.cpp -o enumtostr.o
In file included from muscle.h:34:0,
from enumtostr.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c estring.cpp -o estring.o
estring.cpp:464:13: warning: ‘bool CanMultiplyEstrings(const short int*, const short int*)’ defined but not used [-Wunused-function]
static bool CanMultiplyEstrings(const short es1[], const short es2[])
^~~~~~~~~~~~~~~~~~~
In file included from muscle.h:34:0,
from estring.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
estring.cpp: In function ‘void EstringsToPath(const short int*, const short int*, PWPath&)’:
estring.cpp:424:14: warning: ‘cType’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Edge.cType = cType;
~~~~~~~~~~~^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fasta.cpp -o fasta.o
fasta.cpp: In member function ‘void MSA::FromFASTAFile(TextFile&)’:
fasta.cpp:15:11: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
unsigned uSeqCount = 0;
^~~~~~~~~
fasta.cpp:16:11: warning: unused variable ‘uColCount’ [-Wunused-variable]
unsigned uColCount = uInsane;
^~~~~~~~~
In file included from muscle.h:34:0,
from fasta.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fasta2.cpp -o fasta2.o
In file included from muscle.h:34:0,
from fasta2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastclust.cpp -o fastclust.o
In file included from muscle.h:34:0,
from fastclust.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastdist.cpp -o fastdist.o
In file included from muscle.h:34:0,
from fastdist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastdistjones.cpp -o fastdistjones.o
In file included from muscle.h:34:0,
from fastdistjones.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastdistkbit.cpp -o fastdistkbit.o
In file included from muscle.h:34:0,
from fastdistkbit.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function ‘void FastDistKmer(const SeqVect&, DistFunc&)’:
fastdistkmer.cpp:235:11: warning: unused variable ‘KD’ [-Wunused-variable]
double KD = KimuraDist(EstimatedPctId);
^~
In file included from muscle.h:34:0,
from fastdistkmer.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function ‘void DistKmer6_6(const SeqVect&, DistFunc&)’:
fastdistmafft.cpp:238:15: warning: unused variable ‘pName1’ [-Wunused-variable]
const char *pName1 = s1.GetName();
^~~~~~
fastdistmafft.cpp: At global scope:
fastdistmafft.cpp:104:13: warning: ‘void ListCount(const unsigned char*)’ defined but not used [-Wunused-function]
static void ListCount(const unsigned char Count[])
^~~~~~~~~
In file included from muscle.h:34:0,
from fastdistmafft.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function ‘void DistKmer4_6(const SeqVect&, DistFunc&)’:
fastdistnuc.cpp:223:15: warning: unused variable ‘pName1’ [-Wunused-variable]
const char *pName1 = s1.GetName();
^~~~~~
fastdistnuc.cpp: At global scope:
fastdistnuc.cpp:85:13: warning: ‘void ListCount(const unsigned char*)’ defined but not used [-Wunused-function]
static void ListCount(const unsigned char Count[])
^~~~~~~~~
fastdistnuc.cpp:33:17: warning: ‘uResidueGroupCount’ defined but not used [-Wunused-variable]
static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
^~~~~~~~~~~~~~~~~~
In file included from muscle.h:34:0,
from fastdistnuc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastscorepath2.cpp -o fastscorepath2.o
In file included from muscle.h:34:0,
from fastscorepath2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c finddiags.cpp -o finddiags.o
finddiags.cpp:11:14: warning: ‘char* TupleToStr(int)’ defined but not used [-Wunused-function]
static char *TupleToStr(int t)
^~~~~~~~~~
In file included from muscle.h:34:0,
from finddiags.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function ‘char* TupleToStr(int)’:
finddiagsn.cpp:16:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < K; ++i)
~~^~~
finddiagsn.cpp: At global scope:
finddiagsn.cpp:12:14: warning: ‘char* TupleToStr(int)’ defined but not used [-Wunused-function]
static char *TupleToStr(int t)
^~~~~~~~~~
In file included from muscle.h:34:0,
from finddiagsn.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalign.cpp -o glbalign.o
In file included from muscle.h:34:0,
from glbalign.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalign352.cpp -o glbalign352.o
In file included from muscle.h:34:0,
from glbalign352.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbaligndiag.cpp -o glbaligndiag.o
In file included from muscle.h:34:0,
from glbaligndiag.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalignla.cpp -o glbalignla.o
In file included from muscle.h:34:0,
from glbalignla.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
glbalignla.cpp: In function ‘SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignla.cpp:424:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iTraceBack = (int) uInsertPos - (int) uLengthB;
^~~~~~~~~~~~~~~~
glbalignla.cpp:363:24: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*ptrTraceBack_ij = (int) uInsertPos - (int) j;
^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalignle.cpp -o glbalignle.o
In file included from muscle.h:34:0,
from glbalignle.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
glbalignle.cpp: In function ‘SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignle.cpp:427:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iTraceBack = (int) uInsertPos - (int) uLengthB;
^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalignns.cpp -o glbalignns.o
In file included from muscle.h:34:0,
from glbalignns.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
glbalignns.cpp: In function ‘SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignns.cpp:366:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iTraceBack = (int) uInsertPos - (int) uLengthB;
^~~~~~~~~~~~~~~~
glbalignns.cpp:305:24: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*ptrTraceBack_ij = (int) uInsertPos - (int) j;
^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalignsimple.cpp -o glbalignsimple.o
glbalignsimple.cpp:52:13: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
^~~~~~
glbalignsimple.cpp:28:13: warning: ‘void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
^~~~~~
In file included from muscle.h:34:0,
from glbalignsimple.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalignsp.cpp -o glbalignsp.o
In file included from muscle.h:34:0,
from glbalignsp.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
glbalignsp.cpp: In function ‘SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignsp.cpp:366:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iTraceBack = (int) uInsertPos - (int) uLengthB;
^~~~~~~~~~~~~~~~
glbalignsp.cpp:305:24: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*ptrTraceBack_ij = (int) uInsertPos - (int) j;
^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalignspn.cpp -o glbalignspn.o
In file included from muscle.h:34:0,
from glbalignspn.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
glbalignspn.cpp: In function ‘SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignspn.cpp:401:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iTraceBack = (int) uInsertPos - (int) uLengthB;
^~~~~~~~~~~~~~~~
glbalignspn.cpp:340:24: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*ptrTraceBack_ij = (int) uInsertPos - (int) j;
^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’:
glbalignss.cpp:177:16: warning: unused variable ‘ptrRowA’ [-Wunused-variable]
const SCORE *ptrRowA = MxRowA[i];
^~~~~~~
glbalignss.cpp:119:17: warning: unused variable ‘uPrefixCountA’ [-Wunused-variable]
const unsigned uPrefixCountA = uLengthA + 1;
^~~~~~~~~~~~~
glbalignss.cpp:120:17: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
const unsigned uPrefixCountB = uLengthB + 1;
^~~~~~~~~~~~~
glbalignss.cpp: At global scope:
glbalignss.cpp:11:14: warning: ‘SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
^~~~~
In file included from muscle.h:34:0,
from glbalignss.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’:
glbalignss.cpp:310:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iTraceBack = (int) uInsertPos - (int) uLengthB;
^~~~~~~~~~~~~~~~
glbalignss.cpp:252:24: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*ptrTraceBack_ij = (int) uInsertPos - (int) j;
^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function ‘SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)’:
glbalndimer.cpp:123:9: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch]
switch (g_PPScore)
^
glbalndimer.cpp:123:9: warning: enumeration value ‘PPSCORE_SPN’ not handled in switch [-Wswitch]
glbalndimer.cpp: At global scope:
glbalndimer.cpp:14:20: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
^~~~~~~~~~~~~~~
In file included from muscle.h:34:0,
from glbalndimer.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c globals.cpp -o globals.o
In file included from muscle.h:34:0,
from globals.cpp:6:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c globalslinux.cpp -o globalslinux.o
globalslinux.cpp: In function ‘double GetNAN()’:
globalslinux.cpp:21:28: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
double dNAN = *( double* )nan;
^~~
In file included from muscle.h:34:0,
from globalslinux.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c globalsosx.cpp -o globalsosx.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c globalsother.cpp -o globalsother.o
In file included from muscle.h:34:0,
from globalsother.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c globalswin32.cpp -o globalswin32.o
In file included from muscle.h:34:0,
from globalswin32.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gonnet.cpp -o gonnet.o
gonnet.cpp:137:14: warning: ‘Gonnet160’ defined but not used [-Wunused-variable]
static SCORE Gonnet160[20][20] =
^~~~~~~~~
In file included from muscle.h:34:0,
from gonnet.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gotowt.cpp -o gotowt.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c henikoffweight.cpp -o henikoffweight.o
In file included from muscle.h:34:0,
from henikoffweight.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c henikoffweightpb.cpp -o henikoffweightpb.o
In file included from muscle.h:34:0,
from henikoffweightpb.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c html.cpp -o html.o
In file included from muscle.h:34:0,
from html.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hydro.cpp -o hydro.o
In file included from muscle.h:34:0,
from hydro.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c intmath.cpp -o intmath.o
In file included from muscle.h:34:0,
from intmath.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c local.cpp -o local.o
In file included from muscle.h:34:0,
from local.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c main.cpp -o main.o
In file included from muscle.h:34:0,
from main.cpp:7:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’:
makerootmsa.cpp:18:17: warning: unused variable ‘uSeqLength’ [-Wunused-variable]
const unsigned uSeqLength = s.Length();
^~~~~~~~~~
makerootmsa.cpp: In function ‘short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)’:
makerootmsa.cpp:94:17: warning: unused variable ‘Path’ [-Wunused-variable]
const PWPath &Path = Nodes[uNodeIndex].m_Path;
^~~~
makerootmsa.cpp: In function ‘void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)’:
makerootmsa.cpp:168:17: warning: unused variable ‘uTreeNodeCount’ [-Wunused-variable]
const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
^~~~~~~~~~~~~~
makerootmsa.cpp: At global scope:
makerootmsa.cpp:12:13: warning: ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’ defined but not used [-Wunused-function]
static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
^~~~~~~
In file included from muscle.h:34:0,
from makerootmsa.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c makerootmsab.cpp -o makerootmsab.o
In file included from muscle.h:34:0,
from makerootmsab.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c maketree.cpp -o maketree.o
In file included from muscle.h:34:0,
from maketree.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mhack.cpp -o mhack.o
In file included from muscle.h:34:0,
from mhack.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mpam200.cpp -o mpam200.o
In file included from muscle.h:34:0,
from mpam200.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c msa.cpp -o msa.o
msa.cpp:419:13: warning: ‘void FmtPad(unsigned int)’ defined but not used [-Wunused-function]
static void FmtPad(unsigned n)
^~~~~~
msa.cpp:407:13: warning: ‘void FmtInt0(unsigned int, unsigned int)’ defined but not used [-Wunused-function]
static void FmtInt0(unsigned u, unsigned uWidth)
^~~~~~~
msa.cpp:392:13: warning: ‘void FmtInt(unsigned int, unsigned int)’ defined but not used [-Wunused-function]
static void FmtInt(unsigned u, unsigned uWidth)
^~~~~~
msa.cpp:385:13: warning: ‘void FmtChar(char, unsigned int)’ defined but not used [-Wunused-function]
static void FmtChar(char c, unsigned uWidth)
^~~~~~~
In file included from muscle.h:34:0,
from msa.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c msa2.cpp -o msa2.o
msa2.cpp: In function ‘void SetMSAWeightsMuscle(MSA&)’:
msa2.cpp:357:9: warning: enumeration value ‘SEQWEIGHT_Undefined’ not handled in switch [-Wswitch]
switch (Method)
^
msa2.cpp: In function ‘void MSAAppend(MSA&, const MSA&)’:
msa2.cpp:476:17: warning: unused variable ‘uColCountCat’ [-Wunused-variable]
const unsigned uColCountCat = uColCount1 + uColCount2;
^~~~~~~~~~~~
In file included from muscle.h:34:0,
from msa2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c msadistkimura.cpp -o msadistkimura.o
In file included from muscle.h:34:0,
from msadistkimura.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c msf.cpp -o msf.o
msf.cpp:24:20: warning: ‘const char* strfind(const char*, const char*)’ defined but not used [-Wunused-function]
static const char *strfind(const char *s, const char *t)
^~~~~~~
In file included from muscle.h:34:0,
from msf.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c muscle.cpp -o muscle.o
In file included from muscle.h:34:0,
from muscle.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c muscleout.cpp -o muscleout.o
In file included from muscle.h:34:0,
from muscleout.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nucmx.cpp -o nucmx.o
In file included from muscle.h:34:0,
from nucmx.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nwdasimple.cpp -o nwdasimple.o
In file included from muscle.h:34:0,
from nwdasimple.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nwdasimple2.cpp -o nwdasimple2.o
In file included from muscle.h:34:0,
from nwdasimple2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nwdasmall.cpp -o nwdasmall.o
In file included from muscle.h:34:0,
from nwdasmall.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nwrec.cpp -o nwrec.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nwsmall.cpp -o nwsmall.o
In file included from muscle.h:34:0,
from nwsmall.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c objscore.cpp -o objscore.o
objscore.cpp: In function ‘SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)’:
objscore.cpp:31:9: warning: enumeration value ‘OBJSCORE_Undefined’ not handled in switch [-Wswitch]
switch (OS)
^
objscore.cpp:31:9: warning: enumeration value ‘OBJSCORE_SPM’ not handled in switch [-Wswitch]
In file included from muscle.h:34:0,
from objscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function ‘SCORE TermGapScore(bool)’:
objscore2.cpp:22:9: warning: enumeration value ‘TERMGAPS_Undefined’ not handled in switch [-Wswitch]
switch (g_TermGaps)
^
objscore2.cpp: In function ‘SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)’:
objscore2.cpp:62:8: warning: unused variable ‘scoreGaps’ [-Wunused-variable]
SCORE scoreGaps = 0;
^~~~~~~~~
objscore2.cpp:63:7: warning: unused variable ‘bGapping1’ [-Wunused-variable]
bool bGapping1 = false;
^~~~~~~~~
objscore2.cpp:64:7: warning: unused variable ‘bGapping2’ [-Wunused-variable]
bool bGapping2 = false;
^~~~~~~~~
objscore2.cpp:67:7: warning: variable ‘bLeftTermGap’ set but not used [-Wunused-but-set-variable]
bool bLeftTermGap = false;
^~~~~~~~~~~~
objscore2.cpp:82:7: warning: variable ‘bRightTermGap’ set but not used [-Wunused-but-set-variable]
bool bRightTermGap = false;
^~~~~~~~~~~~~
objscore2.cpp: In function ‘SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)’:
objscore2.cpp:140:7: warning: variable ‘bLeftTermGap’ set but not used [-Wunused-but-set-variable]
bool bLeftTermGap = false;
^~~~~~~~~~~~
objscore2.cpp:155:7: warning: variable ‘bRightTermGap’ set but not used [-Wunused-but-set-variable]
bool bRightTermGap = false;
^~~~~~~~~~~~~
objscore2.cpp: In function ‘SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)’:
objscore2.cpp:314:17: warning: unused variable ‘uColCount2’ [-Wunused-variable]
const unsigned uColCount2 = msa2.GetColCount();
^~~~~~~~~~
objscore2.cpp: In function ‘SCORE ObjScoreXP(const MSA&, const MSA&)’:
objscore2.cpp:493:17: warning: unused variable ‘w’ [-Wunused-variable]
const WEIGHT w = w1*w2;
^
In file included from muscle.h:34:0,
from objscore2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c objscoreda.cpp -o objscoreda.o
In file included from muscle.h:34:0,
from objscoreda.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c onexception.cpp -o onexception.o
In file included from muscle.h:34:0,
from onexception.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c optionsR.cpp -o optionsR.o
In file included from muscle.h:34:0,
from optionsR.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c outweights.cpp -o outweights.o
In file included from muscle.h:34:0,
from outweights.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:6:14: warning: ‘PAM200’ defined but not used [-Wunused-variable]
static float PAM200[23][23] =
^~~~~~
In file included from muscle.h:34:0,
from pam200mafft.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c params.cpp -o params.o
params.cpp: In function ‘void SetPPScore(bool)’:
params.cpp:445:9: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch]
switch (g_PPScore)
^
params.cpp: In function ‘void default_params()’:
params.cpp:659:18: warning: statement has no effect [-Wunused-value]
g_ptrScoreMatrix;
^
params.cpp:652:14: warning: unused variable ‘VTML_LA’ [-Wunused-variable]
SCOREMATRIX VTML_LA;
^~~~~~~
params.cpp:653:14: warning: unused variable ‘PAM200’ [-Wunused-variable]
SCOREMATRIX PAM200;
^~~~~~
params.cpp:654:14: warning: unused variable ‘PAM200NoCenter’ [-Wunused-variable]
SCOREMATRIX PAM200NoCenter;
^~~~~~~~~~~~~~
params.cpp:655:14: warning: unused variable ‘VTML_SP’ [-Wunused-variable]
SCOREMATRIX VTML_SP;
^~~~~~~
params.cpp:656:14: warning: unused variable ‘VTML_SPNoCenter’ [-Wunused-variable]
SCOREMATRIX VTML_SPNoCenter;
^~~~~~~~~~~~~~~
params.cpp:657:14: warning: unused variable ‘NUC_SP’ [-Wunused-variable]
SCOREMATRIX NUC_SP;
^~~~~~
In file included from muscle.h:34:0,
from params.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c phy.cpp -o phy.o
phy.cpp: In member function ‘void Tree::RootUnrootedTree(ROOT)’:
phy.cpp:665:9: warning: unused variable ‘dEdgeLength’ [-Wunused-variable]
double dEdgeLength = GetEdgeLength(uNode1, uNode2);
^~~~~~~~~~~
In file included from muscle.h:34:0,
from phy.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c phy2.cpp -o phy2.o
In file included from muscle.h:34:0,
from phy2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c phy3.cpp -o phy3.o
phy3.cpp: In function ‘void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)’:
phy3.cpp:125:15: warning: unused variable ‘dThisDist’ [-Wunused-variable]
const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
^~~~~~~~~
phy3.cpp: In function ‘void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)’:
phy3.cpp:167:17: warning: unused variable ‘uLeafCount’ [-Wunused-variable]
const unsigned uLeafCount = tree.GetLeafCount();
^~~~~~~~~~
phy3.cpp:190:9: warning: unused variable ‘dAllMaxDist’ [-Wunused-variable]
double dAllMaxDist = -1e20;
^~~~~~~~~~~
phy3.cpp:191:11: warning: unused variable ‘uMaxFrom’ [-Wunused-variable]
unsigned uMaxFrom = NULL_NEIGHBOR;
^~~~~~~~
phy3.cpp:192:11: warning: unused variable ‘uMaxTo’ [-Wunused-variable]
unsigned uMaxTo = NULL_NEIGHBOR;
^~~~~~
phy3.cpp: In function ‘void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)’:
phy3.cpp:263:11: warning: variable ‘uMostDistantLeaf’ set but not used [-Wunused-but-set-variable]
unsigned uMostDistantLeaf = NULL_NEIGHBOR;
^~~~~~~~~~~~~~~~
phy3.cpp: At global scope:
phy3.cpp:45:13: warning: ‘void ListEIs(EdgeInfo**, unsigned int)’ defined but not used [-Wunused-function]
static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
^~~~~~~
In file included from muscle.h:34:0,
from phy3.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c phy4.cpp -o phy4.o
In file included from muscle.h:34:0,
from phy4.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c phyfromclust.cpp -o phyfromclust.o
In file included from muscle.h:34:0,
from phyfromclust.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c phyfromfile.cpp -o phyfromfile.o
In file included from muscle.h:34:0,
from phyfromfile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c physeq.cpp -o physeq.o
physeq.cpp: In member function ‘void MSA::ToPhySequentialFile(TextFile&) const’:
physeq.cpp:60:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Col == ColCount)
~~~~^~~~~~~~~~~
physeq.cpp:71:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Col == ColCount)
~~~~^~~~~~~~~~~
physeq.cpp: In member function ‘void MSA::ToPhyInterleavedFile(TextFile&) const’:
physeq.cpp:112:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Col == ColCount)
~~~~^~~~~~~~~~~
physeq.cpp:124:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Col == ColCount)
~~~~^~~~~~~~~~~
In file included from muscle.h:34:0,
from physeq.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c phytofile.cpp -o phytofile.o
In file included from muscle.h:34:0,
from phytofile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c posgap.cpp -o posgap.o
In file included from muscle.h:34:0,
from posgap.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ppscore.cpp -o ppscore.o
In file included from muscle.h:34:0,
from ppscore.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c profdb.cpp -o profdb.o
In file included from clustsetmsa.h:8:0,
from profdb.cpp:9:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
switch(m_Distance)
^
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:34:0,
from profdb.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c profile.cpp -o profile.o
In file included from muscle.h:34:0,
from profile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function ‘void ListProfile(const ProfPos*, unsigned int, const MSA*)’:
profilefrommsa.cpp:131:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (-1 == PP.m_uResidueGroup)
~~~^~~~~~~~~~~~~~~~~~~~~
profilefrommsa.cpp: In function ‘unsigned int ResidueGroupFromFCounts(const FCOUNT*)’:
profilefrommsa.cpp:230:9: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch]
switch (g_Alpha)
^
profilefrommsa.cpp: In function ‘ProfPos* ProfileFromMSA(const MSA&)’:
profilefrommsa.cpp:245:17: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
const unsigned uSeqCount = a.GetSeqCount();
^~~~~~~~~
profilefrommsa.cpp:253:11: warning: unused variable ‘uHydrophobicRunLength’ [-Wunused-variable]
unsigned uHydrophobicRunLength = 0;
^~~~~~~~~~~~~~~~~~~~~
profilefrommsa.cpp: At global scope:
profilefrommsa.cpp:15:20: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
^~~~~~~~~~~~~~~
In file included from muscle.h:34:0,
from profilefrommsa.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c progalign.cpp -o progalign.o
progalign.cpp: In function ‘ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)’:
progalign.cpp:41:17: warning: unused variable ‘uIterCount’ [-Wunused-variable]
const unsigned uIterCount = uSeqCount - 1;
^~~~~~~~~~
In file included from muscle.h:34:0,
from progalign.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c progress.cpp -o progress.o
In file included from muscle.h:34:0,
from progress.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c progressivealign.cpp -o progressivealign.o
In file included from muscle.h:34:0,
from progressivealign.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function ‘void PWPath::Validate() const’:
pwpath.cpp:79:16: warning: unused variable ‘LastEdge’ [-Wunused-variable]
const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
^~~~~~~~
pwpath.cpp: In member function ‘void PWPath::FromFile(TextFile&)’:
pwpath.cpp:212:11: warning: unused variable ‘uEdgeIndex’ [-Wunused-variable]
unsigned uEdgeIndex = 0;
^~~~~~~~~~
In file included from muscle.h:34:0,
from pwpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c readmx.cpp -o readmx.o
readmx.cpp: In function ‘float (* ReadMx(TextFile&))[32][32]’:
readmx.cpp:83:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < MAX_ALPHA; ++i)
~~^~~~~~~~~~~
readmx.cpp:84:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < MAX_ALPHA; ++j)
~~^~~~~~~~~~~
readmx.cpp: At global scope:
readmx.cpp:30:17: warning: ‘unsigned int MxCharToLetter(char)’ defined but not used [-Wunused-function]
static unsigned MxCharToLetter(char c)
^~~~~~~~~~~~~~
In file included from muscle.h:34:0,
from readmx.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c realigndiffs.cpp -o realigndiffs.o
In file included from muscle.h:34:0,
from realigndiffs.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c realigndiffse.cpp -o realigndiffse.o
realigndiffse.cpp: In function ‘void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)’:
realigndiffse.cpp:72:13: warning: unused variable ‘uNewRight’ [-Wunused-variable]
unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
^~~~~~~~~
realigndiffse.cpp:75:13: warning: unused variable ‘uOldRight’ [-Wunused-variable]
unsigned uOldRight = OldTree.GetRight(uOld);
^~~~~~~~~
In file included from muscle.h:34:0,
from realigndiffse.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c redblack.cpp -o redblack.o
In file included from muscle.h:34:0,
from redblack.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c refine.cpp -o refine.o
In file included from clustsetmsa.h:8:0,
from refine.cpp:9:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
switch(m_Distance)
^
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:34:0,
from refine.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c refinehoriz.cpp -o refinehoriz.o
In file included from muscle.h:34:0,
from refinehoriz.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function ‘bool RefineSubfams(MSA&, const Tree&, unsigned int)’:
refinesubfams.cpp:63:17: warning: unused variable ‘uNodeCount’ [-Wunused-variable]
const unsigned uNodeCount = tree.GetNodeCount();
^~~~~~~~~~
In file included from muscle.h:34:0,
from refinesubfams.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c refinetree.cpp -o refinetree.o
In file included from muscle.h:34:0,
from refinetree.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c refinetreee.cpp -o refinetreee.o
In file included from muscle.h:34:0,
from refinetreee.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c refinevert.cpp -o refinevert.o
In file included from muscle.h:34:0,
from refinevert.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c refinew.cpp -o refinew.o
refinew.cpp: In function ‘void AppendMSA(MSA&, const MSA&)’:
refinew.cpp:26:17: warning: unused variable ‘uColCountCat’ [-Wunused-variable]
const unsigned uColCountCat = uColCount1 + uColCount2;
^~~~~~~~~~~~
refinew.cpp: In function ‘void RefineW(const MSA&, MSA&)’:
refinew.cpp:129:13: warning: unused variable ‘uOutCols’ [-Wunused-variable]
unsigned uOutCols = msaOut.GetColCount();
^~~~~~~~
In file included from muscle.h:34:0,
from refinew.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c savebest.cpp -o savebest.o
In file included from muscle.h:34:0,
from savebest.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c scoredist.cpp -o scoredist.o
In file included from muscle.h:34:0,
from scoredist.cpp:3:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c scoregaps.cpp -o scoregaps.o
scoregaps.cpp:80:14: warning: ‘SCORE Penalty(unsigned int, bool)’ defined but not used [-Wunused-function]
static SCORE Penalty(unsigned Length, bool Term)
^~~~~~~
scoregaps.cpp:37:13: warning: ‘void FreeGapInfo(GAPINFO*)’ defined but not used [-Wunused-function]
static void FreeGapInfo(GAPINFO *GI)
^~~~~~~~~~~
In file included from muscle.h:34:0,
from scoregaps.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c scorehistory.cpp -o scorehistory.o
In file included from muscle.h:34:0,
from scorehistory.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c scorepp.cpp -o scorepp.o
In file included from muscle.h:34:0,
from scorepp.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c seq.cpp -o seq.o
In file included from muscle.h:34:0,
from seq.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c seqvect.cpp -o seqvect.o
In file included from muscle.h:34:0,
from seqvect.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c setblosumweights.cpp -o setblosumweights.o
In file included from muscle.h:34:0,
from setblosumweights.cpp:42:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c setgscweights.cpp -o setgscweights.o
In file included from muscle.h:34:0,
from setgscweights.cpp:104:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c setnewhandler.cpp -o setnewhandler.o
In file included from muscle.h:34:0,
from setnewhandler.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c spfast.cpp -o spfast.o
spfast.cpp: In function ‘SCORE ObjScoreSPDimer(const MSA&)’:
spfast.cpp:252:17: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
const unsigned uSeqCount = msa.GetSeqCount();
^~~~~~~~~
spfast.cpp: At global scope:
spfast.cpp:59:14: warning: ‘SCORE SPColBrute(const MSA&, unsigned int)’ defined but not used [-Wunused-function]
static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
^~~~~~~~~~
spfast.cpp:14:20: warning: ‘const char* GapTypeToStr(int)’ defined but not used [-Wunused-function]
static const char *GapTypeToStr(int GapType)
^~~~~~~~~~~~
In file included from muscle.h:34:0,
from spfast.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sptest.cpp -o sptest.o
In file included from muscle.h:34:0,
from sptest.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c stabilize.cpp -o stabilize.o
In file included from muscle.h:34:0,
from stabilize.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c subfam.cpp -o subfam.o
subfam.cpp: In function ‘void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)’:
subfam.cpp:173:6: warning: unused variable ‘NotUsed’ [-Wunused-variable]
int NotUsed = system(CmdLine);
^~~~~~~
In file included from muscle.h:34:0,
from subfam.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c subfams.cpp -o subfams.o
subfams.cpp:52:13: warning: ‘void Relax(DistFunc&, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
static void Relax(DistFunc &DF, unsigned u, unsigned v)
^~~~~
subfams.cpp:40:13: warning: ‘void InitializeSingleSource(DistFunc&, unsigned int)’ defined but not used [-Wunused-function]
static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
^~~~~~~~~~~~~~~~~~~~~~
subfams.cpp:10:13: warning: ‘void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)’ defined but not used [-Wunused-function]
static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
^~~~~~~~~~~~~~~~~~
In file included from muscle.h:34:0,
from subfams.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sw.cpp -o sw.o
sw.cpp:20:13: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
^~~~~~
In file included from muscle.h:34:0,
from sw.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c termgaps.cpp -o termgaps.o
In file included from muscle.h:34:0,
from termgaps.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c textfile.cpp -o textfile.o
textfile.cpp: In member function ‘void TextFile::PutChar(char)’:
textfile.cpp:104:6: warning: unused variable ‘i’ [-Wunused-variable]
int i = fputc(c, m_ptrFile);
^
textfile.cpp: In member function ‘void TextFile::PutString(const char*)’:
textfile.cpp:117:6: warning: unused variable ‘iError’ [-Wunused-variable]
int iError = fputs(szLine, m_ptrFile);
^~~~~~
In file included from muscle.h:34:0,
from textfile.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c threewaywt.cpp -o threewaywt.o
In file included from muscle.h:34:0,
from threewaywt.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tomhydro.cpp -o tomhydro.o
In file included from muscle.h:34:0,
from tomhydro.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c traceback.cpp -o traceback.o
traceback.cpp: In function ‘SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)’:
traceback.cpp:21:17: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
const unsigned uPrefixCountB = uLengthB + 1;
^~~~~~~~~~~~~
In file included from muscle.h:34:0,
from traceback.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
traceback.cpp: In function ‘SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)’:
traceback.cpp:72:3: warning: ‘cPrevEdgeType’ may be used uninitialized in this function [-Wmaybe-uninitialized]
switch (cEdgeType)
^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tracebackopt.cpp -o tracebackopt.o
In file included from muscle.h:34:0,
from tracebackopt.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tracebacksw.cpp -o tracebacksw.o
tracebacksw.cpp: In function ‘void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)’:
tracebacksw.cpp:22:17: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
const unsigned uPrefixCountB = uLengthB + 1;
^~~~~~~~~~~~~
tracebacksw.cpp:29:8: warning: unused variable ‘scoreMax’ [-Wunused-variable]
SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
^~~~~~~~
In file included from muscle.h:34:0,
from tracebacksw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
tracebacksw.cpp: In function ‘void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)’:
tracebacksw.cpp:47:3: warning: ‘cPrevEdgeType’ may be used uninitialized in this function [-Wmaybe-uninitialized]
switch (cEdgeType)
^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c treefrommsa.cpp -o treefrommsa.o
In file included from clustsetmsa.h:8:0,
from treefrommsa.cpp:5:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
switch(m_Distance)
^
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:34:0,
from treefrommsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c typetostr.cpp -o typetostr.o
In file included from muscle.h:34:0,
from typetostr.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
typetostr.cpp: In function ‘const char* SecsToStr(long unsigned int)’:
typetostr.cpp:4:13: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=]
const char *SecsToStr(unsigned long Secs)
^~~~~~~~~
typetostr.cpp:4:13: note: directive argument in the range [0, 59]
typetostr.cpp:4:13: note: directive argument in the range [0, 59]
In file included from /usr/include/stdio.h:862:0,
from muscle.h:27,
from typetostr.cpp:1:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 9 and 23 bytes into a destination of size 16
__bos (__s), __fmt, __va_arg_pack ());
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c upgma2.cpp -o upgma2.o
upgma2.cpp:68:13: warning: ‘void ListState()’ defined but not used [-Wunused-function]
static void ListState()
^~~~~~~~~
In file included from muscle.h:34:0,
from upgma2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
upgma2.cpp: In function ‘void UPGMA2(const DistCalc&, Tree&, LINKAGE)’:
upgma2.cpp:292:15: warning: ‘dtNewDist’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g_Dist[vL] = dtNewDist;
~~~~~~~~~~~^~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c usage.cpp -o usage.o
In file included from muscle.h:34:0,
from usage.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c validateids.cpp -o validateids.o
In file included from muscle.h:34:0,
from validateids.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vtml2.cpp -o vtml2.o
In file included from muscle.h:34:0,
from vtml2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c writescorefile.cpp -o writescorefile.o
In file included from muscle.h:34:0,
from writescorefile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^~~~~~~~~~~~~
writescorefile.cpp: In function ‘void WriteScoreFile(const MSA&)’:
writescorefile.cpp:40:9: warning: ‘Score’ may be used uninitialized in this function [-Wmaybe-uninitialized]
dSum += Score;
~~~~~^~~~~~~~
writescorefile.cpp:27:11: note: ‘Score’ was declared here
double Score;
^~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o muscle.so aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignla.o glbalignle.o glbalignns.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o gotowt.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o optionsR.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o redblack.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-muscle/00new/muscle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (muscle)
