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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:muscle.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings muscle_3.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/muscle.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘muscle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘muscle’ version ‘3.48.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘muscle’ can be installed ... WARNING
Found the following significant warnings:
  alpha.cpp:84:16: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch]
  clust.cpp:167:16: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch]
  clust.cpp:295:16: warning: enumeration value ‘LINKAGE_Undefined’ not handled in switch [-Wswitch]
  clust.cpp:611:16: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch]
  fastdistjones.cpp:158:18: warning: ‘void operator delete [](void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  glbalndimer.cpp:123:16: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch]
  glbalndimer.cpp:123:16: warning: enumeration value ‘PPSCORE_SPN’ not handled in switch [-Wswitch]
  msa2.cpp:357:16: warning: enumeration value ‘SEQWEIGHT_Undefined’ not handled in switch [-Wswitch]
  objscore.cpp:31:16: warning: enumeration value ‘OBJSCORE_Undefined’ not handled in switch [-Wswitch]
  objscore.cpp:31:16: warning: enumeration value ‘OBJSCORE_SPM’ not handled in switch [-Wswitch]
  objscore2.cpp:22:16: warning: enumeration value ‘TERMGAPS_Undefined’ not handled in switch [-Wswitch]
  params.cpp:445:16: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
  profilefrommsa.cpp:230:16: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch]
  typetostr.cpp:13:28: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/muscle.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/muscle/libs/muscle.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘__vsprintf_chk’, possibly from ‘vsprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/muscle.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL muscle
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘muscle’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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:186:24: 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-3.20-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:58:24: 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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:84:16: 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-3.20-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:162:34: 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-3.20-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:146:14: 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-3.20-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,
                 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-3.20-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]
    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-3.20-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:167:16: 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-3.20-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:284:22: 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-3.20-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,
                 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-3.20-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]
   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-3.20-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,
                 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-3.20-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,
                 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-3.20-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:76:24: 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-3.20-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,
                 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-3.20-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:161:24: 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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:82:40: 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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]
  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-3.20-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:15:18: 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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:235:32: 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-3.20-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:238:29: 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-3.20-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:223:29: 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-3.20-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,
                 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-3.20-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]
   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-3.20-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:16:27: 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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,
                 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-3.20-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]
   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-3.20-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,
                 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-3.20-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,
                 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-3.20-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:177:30: 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-3.20-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:123:16: 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-3.20-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,
                 from globals.cpp:6:
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-3.20-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:21:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   21 |         double dNAN = *( double* )nan;
      |                        ^~~~~~~~~~~~~~
In file included from muscle.h:34,
                 from globalslinux.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-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c globalsosx.cpp -o globalsosx.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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,
                 from globalsother.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-3.20-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,
                 from globalswin32.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-3.20-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]
  137 | static SCORE Gonnet160[20][20] =
      |              ^~~~~~~~~
In file included from muscle.h:34,
                 from gonnet.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-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c gotowt.cpp -o gotowt.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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,
                 from henikoffweight.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-3.20-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,
                 from henikoffweightpb.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-3.20-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,
                 from html.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-3.20-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,
                 from hydro.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-3.20-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,
                 from intmath.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-3.20-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,
                 from local.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-3.20-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,
                 from main.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-3.20-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:18:24: warning: unused variable ‘uSeqLength’ [-Wunused-variable]
   18 |         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:94:31: warning: unused variable ‘Path’ [-Wunused-variable]
   94 |                 const PWPath &Path = Nodes[uNodeIndex].m_Path;
      |                               ^~~~
makerootmsa.cpp: In function ‘void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)’:
makerootmsa.cpp:168:24: warning: unused variable ‘uTreeNodeCount’ [-Wunused-variable]
  168 |         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]
   12 | static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
      |             ^~~~~~~
In file included from muscle.h:34,
                 from makerootmsa.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-3.20-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,
                 from makerootmsab.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-3.20-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,
                 from maketree.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-3.20-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,
                 from mhack.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-3.20-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,
                 from mpam200.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-3.20-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]
  419 | static void FmtPad(unsigned n)
      |             ^~~~~~
msa.cpp:407:13: warning: ‘void FmtInt0(unsigned int, unsigned int)’ defined but not used [-Wunused-function]
  407 | static void FmtInt0(unsigned u, unsigned uWidth)
      |             ^~~~~~~
msa.cpp:392:13: warning: ‘void FmtInt(unsigned int, unsigned int)’ defined but not used [-Wunused-function]
  392 | static void FmtInt(unsigned u, unsigned uWidth)
      |             ^~~~~~
msa.cpp:385:13: warning: ‘void FmtChar(char, unsigned int)’ defined but not used [-Wunused-function]
  385 | static void FmtChar(char c, unsigned uWidth)
      |             ^~~~~~~
In file included from muscle.h:34,
                 from msa.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-3.20-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:357:16: warning: enumeration value ‘SEQWEIGHT_Undefined’ not handled in switch [-Wswitch]
  357 |         switch (Method)
      |                ^
msa2.cpp: In function ‘void MSAAppend(MSA&, const MSA&)’:
msa2.cpp:476:24: warning: unused variable ‘uColCountCat’ [-Wunused-variable]
  476 |         const unsigned uColCountCat = uColCount1 + uColCount2;
      |                        ^~~~~~~~~~~~
In file included from muscle.h:34,
                 from msa2.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-3.20-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,
                 from msadistkimura.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-3.20-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]
   24 | static const char *strfind(const char *s, const char *t)
      |                    ^~~~~~~
In file included from muscle.h:34,
                 from msf.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-3.20-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,
                 from muscle.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-3.20-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,
                 from muscleout.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-3.20-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,
                 from nucmx.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-3.20-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,
                 from nwdasimple.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-3.20-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,
                 from nwdasimple2.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-3.20-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,
                 from nwdasmall.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-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c nwrec.cpp -o nwrec.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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,
                 from nwsmall.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-3.20-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:31:16: warning: enumeration value ‘OBJSCORE_Undefined’ not handled in switch [-Wswitch]
   31 |         switch (OS)
      |                ^
objscore.cpp:31:16: warning: enumeration value ‘OBJSCORE_SPM’ not handled in switch [-Wswitch]
In file included from muscle.h:34,
                 from objscore.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-3.20-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:22:16: warning: enumeration value ‘TERMGAPS_Undefined’ not handled in switch [-Wswitch]
   22 |         switch (g_TermGaps)
      |                ^
objscore2.cpp: In function ‘SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)’:
objscore2.cpp:62:15: warning: unused variable ‘scoreGaps’ [-Wunused-variable]
   62 |         SCORE scoreGaps = 0;
      |               ^~~~~~~~~
objscore2.cpp:63:14: warning: unused variable ‘bGapping1’ [-Wunused-variable]
   63 |         bool bGapping1 = false;
      |              ^~~~~~~~~
objscore2.cpp:64:14: warning: unused variable ‘bGapping2’ [-Wunused-variable]
   64 |         bool bGapping2 = false;
      |              ^~~~~~~~~
objscore2.cpp:67:14: warning: variable ‘bLeftTermGap’ set but not used [-Wunused-but-set-variable]
   67 |         bool bLeftTermGap = false;
      |              ^~~~~~~~~~~~
objscore2.cpp:82:14: warning: variable ‘bRightTermGap’ set but not used [-Wunused-but-set-variable]
   82 |         bool bRightTermGap = false;
      |              ^~~~~~~~~~~~~
objscore2.cpp: In function ‘SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)’:
objscore2.cpp:140:14: warning: variable ‘bLeftTermGap’ set but not used [-Wunused-but-set-variable]
  140 |         bool bLeftTermGap = false;
      |              ^~~~~~~~~~~~
objscore2.cpp:155:14: warning: variable ‘bRightTermGap’ set but not used [-Wunused-but-set-variable]
  155 |         bool bRightTermGap = false;
      |              ^~~~~~~~~~~~~
objscore2.cpp: In function ‘SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)’:
objscore2.cpp:314:24: warning: unused variable ‘uColCount2’ [-Wunused-variable]
  314 |         const unsigned uColCount2 = msa2.GetColCount();
      |                        ^~~~~~~~~~
objscore2.cpp: In function ‘SCORE ObjScoreXP(const MSA&, const MSA&)’:
objscore2.cpp:493:38: warning: unused variable ‘w’ [-Wunused-variable]
  493 |                         const WEIGHT w = w1*w2;
      |                                      ^
In file included from muscle.h:34,
                 from objscore2.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-3.20-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,
                 from objscoreda.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-3.20-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,
                 from onexception.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-3.20-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,
                 from optionsR.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-3.20-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,
                 from outweights.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-3.20-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]
    6 | static float PAM200[23][23] =
      |              ^~~~~~
In file included from muscle.h:34,
                 from pam200mafft.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-3.20-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:445:16: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch]
  445 |         switch (g_PPScore)
      |                ^
params.cpp: In function ‘void default_params()’:
params.cpp:659:9: warning: statement has no effect [-Wunused-value]
  659 |         g_ptrScoreMatrix;
      |         ^~~~~~~~~~~~~~~~
params.cpp:652:21: warning: unused variable ‘VTML_LA’ [-Wunused-variable]
  652 |         SCOREMATRIX VTML_LA;
      |                     ^~~~~~~
params.cpp:653:21: warning: unused variable ‘PAM200’ [-Wunused-variable]
  653 |         SCOREMATRIX PAM200;
      |                     ^~~~~~
params.cpp:654:21: warning: unused variable ‘PAM200NoCenter’ [-Wunused-variable]
  654 |         SCOREMATRIX PAM200NoCenter;
      |                     ^~~~~~~~~~~~~~
params.cpp:655:21: warning: unused variable ‘VTML_SP’ [-Wunused-variable]
  655 |         SCOREMATRIX VTML_SP;
      |                     ^~~~~~~
params.cpp:656:21: warning: unused variable ‘VTML_SPNoCenter’ [-Wunused-variable]
  656 |         SCOREMATRIX VTML_SPNoCenter;
      |                     ^~~~~~~~~~~~~~~
params.cpp:657:21: warning: unused variable ‘NUC_SP’ [-Wunused-variable]
  657 |         SCOREMATRIX NUC_SP;
      |                     ^~~~~~
In file included from muscle.h:34,
                 from params.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-3.20-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:665:16: warning: unused variable ‘dEdgeLength’ [-Wunused-variable]
  665 |         double dEdgeLength = GetEdgeLength(uNode1, uNode2);
      |                ^~~~~~~~~~~
In file included from muscle.h:34,
                 from phy.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-3.20-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,
                 from phy2.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-3.20-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:125:22: warning: unused variable ‘dThisDist’ [-Wunused-variable]
  125 |         const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
      |                      ^~~~~~~~~
phy3.cpp: In function ‘void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)’:
phy3.cpp:167:24: warning: unused variable ‘uLeafCount’ [-Wunused-variable]
  167 |         const unsigned uLeafCount = tree.GetLeafCount();
      |                        ^~~~~~~~~~
phy3.cpp:190:16: warning: unused variable ‘dAllMaxDist’ [-Wunused-variable]
  190 |         double dAllMaxDist = -1e20;
      |                ^~~~~~~~~~~
phy3.cpp:191:18: warning: unused variable ‘uMaxFrom’ [-Wunused-variable]
  191 |         unsigned uMaxFrom = NULL_NEIGHBOR;
      |                  ^~~~~~~~
phy3.cpp:192:18: warning: unused variable ‘uMaxTo’ [-Wunused-variable]
  192 |         unsigned uMaxTo = NULL_NEIGHBOR;
      |                  ^~~~~~
phy3.cpp: In function ‘void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)’:
phy3.cpp:263:18: warning: variable ‘uMostDistantLeaf’ set but not used [-Wunused-but-set-variable]
  263 |         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]
   45 | static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
      |             ^~~~~~~
In file included from muscle.h:34,
                 from phy3.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-3.20-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,
                 from phy4.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-3.20-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,
                 from phyfromclust.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-3.20-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,
                 from phyfromfile.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-3.20-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:60:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   60 |                                 if (Col == ColCount)
      |                                     ~~~~^~~~~~~~~~~
physeq.cpp:71:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   71 |                         if (Col == ColCount)
      |                             ~~~~^~~~~~~~~~~
physeq.cpp: In member function ‘void MSA::ToPhyInterleavedFile(TextFile&) const’:
physeq.cpp:112:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  112 |                                 if (Col == ColCount)
      |                                     ~~~~^~~~~~~~~~~
physeq.cpp:124:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  124 |                 if (Col == ColCount)
      |                     ~~~~^~~~~~~~~~~
In file included from muscle.h:34,
                 from physeq.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-3.20-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,
                 from phytofile.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-3.20-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,
                 from posgap.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-3.20-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,
                 from ppscore.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-3.20-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,
                 from profdb.cpp:9:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
   22 |                 switch(m_Distance)
      |                       ^
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:34,
                 from profdb.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-3.20-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,
                 from profile.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-3.20-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:131:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  131 |                 if (-1 == PP.m_uResidueGroup)
      |                     ~~~^~~~~~~~~~~~~~~~~~~~~
profilefrommsa.cpp: In function ‘unsigned int ResidueGroupFromFCounts(const FCOUNT*)’:
profilefrommsa.cpp:230:16: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch]
  230 |         switch (g_Alpha)
      |                ^
profilefrommsa.cpp: In function ‘ProfPos* ProfileFromMSA(const MSA&)’:
profilefrommsa.cpp:245:24: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
  245 |         const unsigned uSeqCount = a.GetSeqCount();
      |                        ^~~~~~~~~
profilefrommsa.cpp:253:18: warning: unused variable ‘uHydrophobicRunLength’ [-Wunused-variable]
  253 |         unsigned uHydrophobicRunLength = 0;
      |                  ^~~~~~~~~~~~~~~~~~~~~
profilefrommsa.cpp: At global scope:
profilefrommsa.cpp:15:20: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used [-Wunused-function]
   15 | static const char *LocalScoreToStr(SCORE s)
      |                    ^~~~~~~~~~~~~~~
In file included from muscle.h:34,
                 from profilefrommsa.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-3.20-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:41:24: warning: unused variable ‘uIterCount’ [-Wunused-variable]
   41 |         const unsigned uIterCount = uSeqCount - 1;
      |                        ^~~~~~~~~~
In file included from muscle.h:34,
                 from progalign.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-3.20-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,
                 from progress.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-3.20-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,
                 from progressivealign.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-3.20-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:79:23: warning: unused variable ‘LastEdge’ [-Wunused-variable]
   79 |         const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
      |                       ^~~~~~~~
pwpath.cpp: In member function ‘void PWPath::FromFile(TextFile&)’:
pwpath.cpp:212:18: warning: unused variable ‘uEdgeIndex’ [-Wunused-variable]
  212 |         unsigned uEdgeIndex = 0;
      |                  ^~~~~~~~~~
In file included from muscle.h:34,
                 from pwpath.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-3.20-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:83:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   83 |         for (int i = 0; i < MAX_ALPHA; ++i)
      |                         ~~^~~~~~~~~~~
readmx.cpp:84:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   84 |                 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]
   30 | static unsigned MxCharToLetter(char c)
      |                 ^~~~~~~~~~~~~~
In file included from muscle.h:34,
                 from readmx.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-3.20-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,
                 from realigndiffs.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-3.20-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:72:34: warning: unused variable ‘uNewRight’ [-Wunused-variable]
   72 |                         unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
      |                                  ^~~~~~~~~
realigndiffse.cpp:75:34: warning: unused variable ‘uOldRight’ [-Wunused-variable]
   75 |                         unsigned uOldRight = OldTree.GetRight(uOld);
      |                                  ^~~~~~~~~
In file included from muscle.h:34,
                 from realigndiffse.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-3.20-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,
                 from redblack.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-3.20-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,
                 from refine.cpp:9:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
   22 |                 switch(m_Distance)
      |                       ^
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:34,
                 from refine.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-3.20-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,
                 from refinehoriz.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
In function ‘void RefineHeightParts(MSA&, const Tree&, const unsigned int*, bool, bool, unsigned int, ScoreHistory&, bool*, bool*, bool, bool)’,
    inlined from ‘bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)’ at refinehoriz.cpp:259:21:
refinehoriz.cpp:183:58: warning: ‘scoreBefore’ may be used uninitialized [-Wmaybe-uninitialized]
  183 |                 SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore;
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
refinehoriz.cpp: In function ‘bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)’:
refinehoriz.cpp:169:23: note: ‘scoreBefore’ was declared here
  169 |                 SCORE scoreBefore;
      |                       ^~~~~~~~~~~
In function ‘void RefineHeightParts(MSA&, const Tree&, const unsigned int*, bool, bool, unsigned int, ScoreHistory&, bool*, bool*, bool, bool)’,
    inlined from ‘bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)’ at refinehoriz.cpp:259:21:
refinehoriz.cpp:183:58: warning: ‘scoreAfter’ may be used uninitialized [-Wmaybe-uninitialized]
  183 |                 SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore;
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
refinehoriz.cpp: In function ‘bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)’:
refinehoriz.cpp:170:23: note: ‘scoreAfter’ was declared here
  170 |                 SCORE scoreAfter;
      |                       ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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:63:24: warning: unused variable ‘uNodeCount’ [-Wunused-variable]
   63 |         const unsigned uNodeCount = tree.GetNodeCount();
      |                        ^~~~~~~~~~
In file included from muscle.h:34,
                 from refinesubfams.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-3.20-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,
                 from refinetree.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-3.20-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,
                 from refinetreee.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-3.20-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,
                 from refinevert.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-3.20-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:26:24: warning: unused variable ‘uColCountCat’ [-Wunused-variable]
   26 |         const unsigned uColCountCat = uColCount1 + uColCount2;
      |                        ^~~~~~~~~~~~
refinew.cpp: In function ‘void RefineW(const MSA&, MSA&)’:
refinew.cpp:129:34: warning: unused variable ‘uOutCols’ [-Wunused-variable]
  129 |                         unsigned uOutCols = msaOut.GetColCount();
      |                                  ^~~~~~~~
In file included from muscle.h:34,
                 from refinew.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-3.20-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,
                 from savebest.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-3.20-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,
                 from scoredist.cpp:3:
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-3.20-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]
   80 | static SCORE Penalty(unsigned Length, bool Term)
      |              ^~~~~~~
scoregaps.cpp:37:13: warning: ‘void FreeGapInfo(GAPINFO*)’ defined but not used [-Wunused-function]
   37 | static void FreeGapInfo(GAPINFO *GI)
      |             ^~~~~~~~~~~
In file included from muscle.h:34,
                 from scoregaps.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-3.20-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,
                 from scorehistory.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-3.20-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,
                 from scorepp.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-3.20-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,
                 from seq.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-3.20-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,
                 from seqvect.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-3.20-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,
                 from setblosumweights.cpp:42:
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-3.20-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,
                 from setgscweights.cpp:104:
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-3.20-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,
                 from setnewhandler.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-3.20-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:252:24: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
  252 |         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]
   59 | static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
      |              ^~~~~~~~~~
spfast.cpp:14:20: warning: ‘const char* GapTypeToStr(int)’ defined but not used [-Wunused-function]
   14 | static const char *GapTypeToStr(int GapType)
      |                    ^~~~~~~~~~~~
In file included from muscle.h:34,
                 from spfast.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-3.20-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,
                 from sptest.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-3.20-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,
                 from stabilize.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-3.20-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:173:13: warning: unused variable ‘NotUsed’ [-Wunused-variable]
  173 |         int NotUsed = system(CmdLine);
      |             ^~~~~~~
In file included from muscle.h:34,
                 from subfam.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-3.20-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]
   52 | 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]
   40 | 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]
   10 | static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
      |             ^~~~~~~~~~~~~~~~~~
In file included from muscle.h:34,
                 from subfams.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-3.20-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]
   20 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
In file included from muscle.h:34,
                 from sw.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-3.20-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,
                 from termgaps.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-3.20-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:104:13: warning: unused variable ‘i’ [-Wunused-variable]
  104 |         int i = fputc(c, m_ptrFile);
      |             ^
textfile.cpp: In member function ‘void TextFile::PutString(const char*)’:
textfile.cpp:117:13: warning: unused variable ‘iError’ [-Wunused-variable]
  117 |         int iError = fputs(szLine, m_ptrFile);
      |             ^~~~~~
In file included from muscle.h:34,
                 from textfile.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-3.20-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,
                 from threewaywt.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-3.20-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,
                 from tomhydro.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-3.20-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:21:24: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
   21 |         const unsigned uPrefixCountB = uLengthB + 1;
      |                        ^~~~~~~~~~~~~
In file included from muscle.h:34,
                 from traceback.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-3.20-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,
                 from tracebackopt.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-3.20-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:22:24: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
   22 |         const unsigned uPrefixCountB = uLengthB + 1;
      |                        ^~~~~~~~~~~~~
tracebacksw.cpp:29:15: warning: unused variable ‘scoreMax’ [-Wunused-variable]
   29 |         SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
      |               ^~~~~~~~
In file included from muscle.h:34,
                 from tracebacksw.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-3.20-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,
                 from treefrommsa.cpp:5:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
   22 |                 switch(m_Distance)
      |                       ^
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:34,
                 from treefrommsa.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-3.20-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,
                 from typetostr.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
typetostr.cpp: In function ‘const char* SecsToStr(long unsigned int)’:
typetostr.cpp:13:28: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=]
   13 |         sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss);
      |                            ^
typetostr.cpp:13:22: note: directive argument in the range [0, 59]
   13 |         sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss);
      |                      ^~~~~~~~~~~~~~~~~~~
typetostr.cpp:13:22: note: directive argument in the range [0, 59]
In file included from /usr/include/stdio.h:980,
                 from muscle.h:27:
In function ‘int sprintf(char*, const char*, ...)’,
    inlined from ‘const char* SecsToStr(long unsigned int)’ at typetostr.cpp:13:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 23 bytes into a destination of size 16
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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]
   68 | static void ListState()
      |             ^~~~~~~~~
In file included from muscle.h:34,
                 from upgma2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
upgma2.cpp: In function ‘void UPGMA2(const DistCalc&, Tree&, LINKAGE)’:
upgma2.cpp:292:36: warning: ‘dtNewDist’ may be used uninitialized [-Wmaybe-uninitialized]
  292 |                         g_Dist[vL] = dtNewDist;
      |                         ~~~~~~~~~~~^~~~~~~~~~~
upgma2.cpp:252:32: note: ‘dtNewDist’ was declared here
  252 |                         dist_t dtNewDist;
      |                                ^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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,
                 from usage.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-3.20-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,
                 from validateids.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-3.20-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,
                 from vtml2.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-3.20-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,
                 from writescorefile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
In function ‘double GetColScore(const MSA&, unsigned int)’,
    inlined from ‘void WriteScoreFile(const MSA&)’ at writescorefile.cpp:59:29:
writescorefile.cpp:40:30: warning: ‘Score’ may be used uninitialized [-Wmaybe-uninitialized]
   40 |                         dSum += Score;
      |                         ~~~~~^~~~~~~~
writescorefile.cpp: In function ‘void WriteScoreFile(const MSA&)’:
writescorefile.cpp:27:32: note: ‘Score’ was declared here
   27 |                         double Score;
      |                                ^~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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)