##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL muscle
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘muscle’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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:186:24: warning: unused variable ‘uLengthA’ [-Wunused-variable]
186 | const unsigned uLengthA = msaA.GetColCount();
| ^~~~~~~~
aligngivenpath.cpp:187:24: warning: unused variable ‘uLengthB’ [-Wunused-variable]
187 | const unsigned uLengthB = msaB.GetColCount();
| ^~~~~~~~
aligngivenpath.cpp: In function ‘void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpath.cpp:335:40: warning: unused variable ‘uColA’ [-Wunused-variable]
335 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
aligngivenpath.cpp:336:40: warning: unused variable ‘uColB’ [-Wunused-variable]
336 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
aligngivenpath.cpp:346:40: warning: unused variable ‘uColA’ [-Wunused-variable]
346 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
aligngivenpath.cpp:354:40: warning: unused variable ‘uColB’ [-Wunused-variable]
354 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
In file included from muscle.h:34,
from aligngivenpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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:58:24: warning: unused variable ‘uLengthA’ [-Wunused-variable]
58 | const unsigned uLengthA = msaA.GetColCount();
| ^~~~~~~~
aligngivenpathsw.cpp:59:24: warning: unused variable ‘uLengthB’ [-Wunused-variable]
59 | const unsigned uLengthB = msaB.GetColCount();
| ^~~~~~~~
aligngivenpathsw.cpp: In function ‘void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpathsw.cpp:204:40: warning: unused variable ‘uColA’ [-Wunused-variable]
204 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
aligngivenpathsw.cpp:205:40: warning: unused variable ‘uColB’ [-Wunused-variable]
205 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
aligngivenpathsw.cpp:215:40: warning: unused variable ‘uColA’ [-Wunused-variable]
215 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
aligngivenpathsw.cpp:223:40: warning: unused variable ‘uColB’ [-Wunused-variable]
223 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
In file included from muscle.h:34,
from aligngivenpathsw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c aligntwomsas.cpp -o aligntwomsas.o
In file included from muscle.h:34,
from aligntwomsas.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c aligntwoprofs.cpp -o aligntwoprofs.o
In file included from muscle.h:34,
from aligntwoprofs.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c aln.cpp -o aln.o
In file included from muscle.h:34,
from aln.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c alpha.cpp -o alpha.o
alpha.cpp: In function ‘unsigned int GetAlphaSize(ALPHA)’:
alpha.cpp:84:16: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch]
84 | switch (Alpha)
| ^
In file included from muscle.h:34,
from alpha.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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:162:34: warning: unused variable ‘uWindowCenter’ [-Wunused-variable]
162 | 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]
105 | 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]
53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
| ^~~~~~~~~~~~~~~~~
In file included from muscle.h:34,
from anchors.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function ‘void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)’:
bittraceback.cpp:146:14: warning: unused variable ‘Bits’ [-Wunused-variable]
146 | 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]
15 | static const char *BitsToStr(char Bits)
| ^~~~~~~~~
In file included from muscle.h:34,
from bittraceback.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c blosum62.cpp -o blosum62.o
In file included from muscle.h:34,
from blosum62.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c blosumla.cpp -o blosumla.o
blosumla.cpp:7:14: warning: ‘Blosum62LA’ defined but not used [-Wunused-variable]
7 | static float Blosum62LA[20][20] =
| ^~~~~~~~~~
In file included from muscle.h:34,
from blosumla.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c clust.cpp -o clust.o
clust.cpp: In member function ‘void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:167:16: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch]
167 | switch (m_JoinStyle)
| ^
clust.cpp: In member function ‘void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:184:24: warning: unused variable ‘uClusterCount’ [-Wunused-variable]
184 | const unsigned uClusterCount = GetClusterCount();
| ^~~~~~~~~~~~~
clust.cpp: In member function ‘void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:204:24: warning: unused variable ‘uClusterCount’ [-Wunused-variable]
204 | const unsigned uClusterCount = GetClusterCount();
| ^~~~~~~~~~~~~
clust.cpp: In member function ‘float Clust::ComputeDist(unsigned int, unsigned int)’:
clust.cpp:295:16: warning: enumeration value ‘LINKAGE_Undefined’ not handled in switch [-Wswitch]
295 | switch (m_CentroidStyle)
| ^
clust.cpp: In member function ‘float Clust::ComputeDistMAFFT(unsigned int, unsigned int)’:
clust.cpp:360:21: warning: unused variable ‘dDistLR’ [-Wunused-variable]
360 | const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
| ^~~~~~~
clust.cpp: In member function ‘float Clust::ComputeMetric(unsigned int, unsigned int) const’:
clust.cpp:611:16: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch]
611 | switch (m_JoinStyle)
| ^
In file included from muscle.h:34,
from clust.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c cluster.cpp -o cluster.o
cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’:
cluster.cpp:284:22: warning: variable ‘bFound’ set but not used [-Wunused-but-set-variable]
284 | bool bFound = false;
| ^~~~~~
cluster.cpp:267:16: warning: unused variable ‘dMaxDist’ [-Wunused-variable]
267 | double dMaxDist = 0.0;
| ^~~~~~~~
In file included from muscle.h:34,
from cluster.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’:
cluster.cpp:307:47: warning: ‘uIndexClosest1’ may be used uninitialized [-Wmaybe-uninitialized]
307 | ClusterNode &Child1 = m_Nodes[uIndexClosest1];
| ^~~~~~~~~~~~~~
cluster.cpp:282:26: note: ‘uIndexClosest1’ was declared here
282 | unsigned uIndexClosest1;
| ^~~~~~~~~~~~~~
cluster.cpp:308:47: warning: ‘uIndexClosest2’ may be used uninitialized [-Wmaybe-uninitialized]
308 | ClusterNode &Child2 = m_Nodes[uIndexClosest2];
| ^~~~~~~~~~~~~~
cluster.cpp:283:26: note: ‘uIndexClosest2’ was declared here
283 | unsigned uIndexClosest2;
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c clwwt.cpp -o clwwt.o
In file included from muscle.h:34,
from clwwt.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c color.cpp -o color.o
color.cpp:72:12: warning: ‘int BlosumScore(char, char)’ defined but not used [-Wunused-function]
72 | static int BlosumScore(char c1, char c2)
| ^~~~~~~~~~~
In file included from muscle.h:34,
from color.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c cons.cpp -o cons.o
In file included from muscle.h:34,
from cons.cpp:7:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c diaglist.cpp -o diaglist.o
In file included from muscle.h:34,
from diaglist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
diaglist.cpp: In member function ‘void DiagList::FromPath(const PWPath&)’:
diaglist.cpp:70:36: warning: ‘uStartPosA’ may be used uninitialized [-Wmaybe-uninitialized]
70 | Add(uStartPosA, uStartPosB, uLength);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diaglist.cpp:51:18: note: ‘uStartPosA’ was declared here
51 | unsigned uStartPosA;
| ^~~~~~~~~~
diaglist.cpp:70:36: warning: ‘uStartPosB’ may be used uninitialized [-Wmaybe-uninitialized]
70 | Add(uStartPosA, uStartPosB, uLength);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diaglist.cpp:52:18: note: ‘uStartPosB’ was declared here
52 | unsigned uStartPosB;
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function ‘SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)’:
diffobjscore.cpp:76:24: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
76 | const unsigned uSeqCount = msa.GetSeqCount();
| ^~~~~~~~~
diffobjscore.cpp:77:24: warning: unused variable ‘uColCount’ [-Wunused-variable]
77 | const unsigned uColCount = msa.GetColCount();
| ^~~~~~~~~
In file included from muscle.h:34,
from diffobjscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c diffpaths.cpp -o diffpaths.o
In file included from muscle.h:34,
from diffpaths.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function ‘void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)’:
difftrees.cpp:161:24: warning: unused variable ‘uLeafCount2’ [-Wunused-variable]
161 | const unsigned uLeafCount2 = Tree2.GetLeafCount();
| ^~~~~~~~~~~
In file included from muscle.h:34,
from difftrees.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c difftreese.cpp -o difftreese.o
In file included from muscle.h:34,
from difftreese.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c distcalc.cpp -o distcalc.o
In file included from muscle.h:34,
from distcalc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c distfunc.cpp -o distfunc.o
In file included from muscle.h:34,
from distfunc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c distpwkimura.cpp -o distpwkimura.o
In file included from muscle.h:34,
from distpwkimura.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c domuscle.cpp -o domuscle.o
In file included from muscle.h:34,
from domuscle.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c dosp.cpp -o dosp.o
In file included from muscle.h:34,
from dosp.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function ‘void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)’:
dpreglist.cpp:82:40: warning: unused variable ‘uDiagLengthMinusCaps’ [-Wunused-variable]
82 | const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
| ^~~~~~~~~~~~~~~~~~~~
In file included from muscle.h:34,
from dpreglist.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c drawtree.cpp -o drawtree.o
In file included from muscle.h:34,
from drawtree.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c edgelist.cpp -o edgelist.o
In file included from muscle.h:34,
from edgelist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c enumopts.cpp -o enumopts.o
In file included from muscle.h:34,
from enumopts.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c enumtostr.cpp -o enumtostr.o
In file included from muscle.h:34,
from enumtostr.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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]
464 | static bool CanMultiplyEstrings(const short es1[], const short es2[])
| ^~~~~~~~~~~~~~~~~~~
In file included from muscle.h:34,
from estring.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
estring.cpp: In function ‘void EstringsToPath(const short int*, const short int*, PWPath&)’:
estring.cpp:409:17: warning: ‘cType’ may be used uninitialized [-Wmaybe-uninitialized]
409 | switch (cType)
| ^~~~~~
estring.cpp:377:22: note: ‘cType’ was declared here
377 | char cType;
| ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fasta.cpp -o fasta.o
fasta.cpp: In member function ‘void MSA::FromFASTAFile(TextFile&)’:
fasta.cpp:15:18: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
15 | unsigned uSeqCount = 0;
| ^~~~~~~~~
fasta.cpp:16:18: warning: unused variable ‘uColCount’ [-Wunused-variable]
16 | unsigned uColCount = uInsane;
| ^~~~~~~~~
In file included from muscle.h:34,
from fasta.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fasta2.cpp -o fasta2.o
In file included from muscle.h:34,
from fasta2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fastclust.cpp -o fastclust.o
In file included from muscle.h:34,
from fastclust.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fastdist.cpp -o fastdist.o
In file included from muscle.h:34,
from fastdist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fastdistjones.cpp -o fastdistjones.o
In file included from muscle.h:34,
from fastdistjones.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
fastdistjones.cpp: In function ‘void DistKmer20_3(const SeqVect&, DistFunc&)’:
fastdistjones.cpp:158:18: warning: ‘void operator delete [](void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
158 | delete[] SeqList;
| ^~~~~~~
fastdistjones.cpp:121:60: note: returned from ‘void* malloc(size_t)’
121 | unsigned short *SeqList = (unsigned short *) malloc(uSeqListBytes);
| ~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fastdistkbit.cpp -o fastdistkbit.o
In file included from muscle.h:34,
from fastdistkbit.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function ‘void FastDistKmer(const SeqVect&, DistFunc&)’:
fastdistkmer.cpp:235:32: warning: unused variable ‘KD’ [-Wunused-variable]
235 | double KD = KimuraDist(EstimatedPctId);
| ^~
In file included from muscle.h:34,
from fastdistkmer.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function ‘void DistKmer6_6(const SeqVect&, DistFunc&)’:
fastdistmafft.cpp:238:29: warning: unused variable ‘pName1’ [-Wunused-variable]
238 | 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]
104 | static void ListCount(const unsigned char Count[])
| ^~~~~~~~~
In file included from muscle.h:34,
from fastdistmafft.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function ‘void DistKmer4_6(const SeqVect&, DistFunc&)’:
fastdistnuc.cpp:223:29: warning: unused variable ‘pName1’ [-Wunused-variable]
223 | 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]
85 | static void ListCount(const unsigned char Count[])
| ^~~~~~~~~
fastdistnuc.cpp:33:17: warning: ‘uResidueGroupCount’ defined but not used [-Wunused-variable]
33 | static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
| ^~~~~~~~~~~~~~~~~~
In file included from muscle.h:34,
from fastdistnuc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fastscorepath2.cpp -o fastscorepath2.o
In file included from muscle.h:34,
from fastscorepath2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c finddiags.cpp -o finddiags.o
finddiags.cpp:11:14: warning: ‘char* TupleToStr(int)’ defined but not used [-Wunused-function]
11 | static char *TupleToStr(int t)
| ^~~~~~~~~~
In file included from muscle.h:34,
from finddiags.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function ‘char* TupleToStr(int)’:
finddiagsn.cpp:16:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
16 | 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]
12 | static char *TupleToStr(int t)
| ^~~~~~~~~~
In file included from muscle.h:34,
from finddiagsn.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalign.cpp -o glbalign.o
In file included from muscle.h:34,
from glbalign.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalign352.cpp -o glbalign352.o
In file included from muscle.h:34,
from glbalign352.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbaligndiag.cpp -o glbaligndiag.o
In file included from muscle.h:34,
from glbaligndiag.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalignla.cpp -o glbalignla.o
In file included from muscle.h:34,
from glbalignla.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalignla.cpp: In function ‘SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignla.cpp:363:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
363 | *ptrTraceBack_ij = (int) uInsertPos - (int) j;
| ^~~~~~~~~~~~~~~~
glbalignla.cpp:330:26: note: ‘uInsertPos’ was declared here
330 | unsigned uInsertPos;
| ^~~~~~~~~~
glbalignla.cpp:424:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
424 | iTraceBack = (int) uInsertPos - (int) uLengthB;
| ^~~~~~~~~~~~~~~~
glbalignla.cpp:397:18: note: ‘uInsertPos’ was declared here
397 | unsigned uInsertPos;
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalignle.cpp -o glbalignle.o
In file included from muscle.h:34,
from glbalignle.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalignle.cpp: In function ‘SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignle.cpp:427:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
427 | iTraceBack = (int) uInsertPos - (int) uLengthB;
| ^~~~~~~~~~~~~~~~
glbalignle.cpp:400:18: note: ‘uInsertPos’ was declared here
400 | unsigned uInsertPos;
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalignns.cpp -o glbalignns.o
In file included from muscle.h:34,
from glbalignns.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalignns.cpp: In function ‘SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignns.cpp:305:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
305 | *ptrTraceBack_ij = (int) uInsertPos - (int) j;
| ^~~~~~~~~~~~~~~~
glbalignns.cpp:272:26: note: ‘uInsertPos’ was declared here
272 | unsigned uInsertPos;
| ^~~~~~~~~~
glbalignns.cpp:366:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
366 | iTraceBack = (int) uInsertPos - (int) uLengthB;
| ^~~~~~~~~~~~~~~~
glbalignns.cpp:339:18: note: ‘uInsertPos’ was declared here
339 | unsigned uInsertPos;
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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]
52 | 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]
28 | static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
| ^~~~~~
In file included from muscle.h:34,
from glbalignsimple.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalignsp.cpp -o glbalignsp.o
In file included from muscle.h:34,
from glbalignsp.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalignsp.cpp: In function ‘SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignsp.cpp:305:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
305 | *ptrTraceBack_ij = (int) uInsertPos - (int) j;
| ^~~~~~~~~~~~~~~~
glbalignsp.cpp:272:26: note: ‘uInsertPos’ was declared here
272 | unsigned uInsertPos;
| ^~~~~~~~~~
glbalignsp.cpp:366:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
366 | iTraceBack = (int) uInsertPos - (int) uLengthB;
| ^~~~~~~~~~~~~~~~
glbalignsp.cpp:339:18: note: ‘uInsertPos’ was declared here
339 | unsigned uInsertPos;
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalignspn.cpp -o glbalignspn.o
In file included from muscle.h:34,
from glbalignspn.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalignspn.cpp: In function ‘SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignspn.cpp:340:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
340 | *ptrTraceBack_ij = (int) uInsertPos - (int) j;
| ^~~~~~~~~~~~~~~~
glbalignspn.cpp:307:26: note: ‘uInsertPos’ was declared here
307 | unsigned uInsertPos;
| ^~~~~~~~~~
glbalignspn.cpp:401:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
401 | iTraceBack = (int) uInsertPos - (int) uLengthB;
| ^~~~~~~~~~~~~~~~
glbalignspn.cpp:374:18: note: ‘uInsertPos’ was declared here
374 | unsigned uInsertPos;
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’:
glbalignss.cpp:177:30: warning: unused variable ‘ptrRowA’ [-Wunused-variable]
177 | const SCORE *ptrRowA = MxRowA[i];
| ^~~~~~~
glbalignss.cpp:119:24: warning: unused variable ‘uPrefixCountA’ [-Wunused-variable]
119 | const unsigned uPrefixCountA = uLengthA + 1;
| ^~~~~~~~~~~~~
glbalignss.cpp:120:24: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
120 | 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]
11 | static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
| ^~~~~
In file included from muscle.h:34,
from glbalignss.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’:
glbalignss.cpp:252:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
252 | *ptrTraceBack_ij = (int) uInsertPos - (int) j;
| ^~~~~~~~~~~~~~~~
glbalignss.cpp:221:26: note: ‘uInsertPos’ was declared here
221 | unsigned uInsertPos;
| ^~~~~~~~~~
glbalignss.cpp:310:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized]
310 | iTraceBack = (int) uInsertPos - (int) uLengthB;
| ^~~~~~~~~~~~~~~~
glbalignss.cpp:283:18: note: ‘uInsertPos’ was declared here
283 | unsigned uInsertPos;
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function ‘SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)’:
glbalndimer.cpp:123:16: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch]
123 | switch (g_PPScore)
| ^
glbalndimer.cpp:123:16: 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]
14 | static const char *LocalScoreToStr(SCORE s)
| ^~~~~~~~~~~~~~~
In file included from muscle.h:34,
from glbalndimer.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c globals.cpp -o globals.o
globals.cpp: In function ‘void Quit(const char*, ...)’:
globals.cpp:107:9: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
107 | error("error in muscle\n");
| ^~~~~
| perror
In file included from muscle.h:34,
from globals.cpp:6:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:202: globals.o] Error 1
ERROR: compilation failed for package ‘muscle’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/muscle’
* restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/muscle’
