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This page was generated on 2022-01-27 11:07:07 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for enhancerHomologSearch on riesling1


To the developers/maintainers of the enhancerHomologSearch package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/enhancerHomologSearch.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 577/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
enhancerHomologSearch 1.1.0  (landing page)
Jianhong Ou
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/enhancerHomologSearch
git_branch: master
git_last_commit: 603b621
git_last_commit_date: 2021-10-26 13:11:45 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: enhancerHomologSearch
Version: 1.1.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:enhancerHomologSearch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings enhancerHomologSearch_1.1.0.tar.gz
StartedAt: 2022-01-26 18:50:15 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 19:10:56 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 1241.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: enhancerHomologSearch.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:enhancerHomologSearch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings enhancerHomologSearch_1.1.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/enhancerHomologSearch.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'enhancerHomologSearch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'enhancerHomologSearch' version '1.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 whether package 'enhancerHomologSearch' can be installed ... WARNING
Found the following significant warnings:
  Muscle/alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  Muscle/clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  Muscle/clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
  Muscle/clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  Muscle/glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  Muscle/glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
  Muscle/msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
  Muscle/objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch]
  Muscle/objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
  Muscle/objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
  Muscle/params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
  Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
  Muscle/profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
See 'D:/biocbuild/bbs-3.15-bioc/meat/enhancerHomologSearch.Rcheck/00install.out' for details.
* 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 R 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 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 ... NOTE
  Note: found 28 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/enhancerHomologSearch/libs/x64/enhancerHomologSearch.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (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. 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
searchTFBPS     266.19  37.70  304.09
conservedMotifs 179.30  29.71  209.73
saveAlignments    8.03   0.12    8.16
getENCODEdata     3.88   0.36    6.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/enhancerHomologSearch.Rcheck/00check.log'
for details.



Installation output

enhancerHomologSearch.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL enhancerHomologSearch
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'enhancerHomologSearch' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/alignment/Alignment.cpp -o ClustalW/alignment/Alignment.o
ClustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
ClustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
     SeqArray::iterator posToAddTo = sectionToRealign.begin();
                        ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/FileParser.cpp -o ClustalW/fileInput/FileParser.o
ClustalW/fileInput/FileParser.cpp: In member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::__cxx11::string*, ClustalWInput*)':
ClustalW/fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable]
   int n = (*input).inputSeqs.size();
       ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/FileReader.cpp -o ClustalW/fileInput/FileReader.o
ClustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::__cxx11::string*, ClustalWInput*)':
ClustalW/fileInput/FileReader.cpp:421:10: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable]
      int maxAlnLength; // Get values from the Alignment object.
          ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/Utility.cpp -o ClustalW/general/Utility.o
ClustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
ClustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
    int n;
        ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/Help.cpp -o ClustalW/Help.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/multipleAlign/Iteration.cpp -o ClustalW/multipleAlign/Iteration.o
ClustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
ClustalW/multipleAlign/Iteration.cpp:171:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
     int count;
         ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/multipleAlign/MSA.cpp -o ClustalW/multipleAlign/MSA.o
ClustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
ClustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
       int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
           ^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/substitutionMatrix/SubMatrix.cpp -o ClustalW/substitutionMatrix/SubMatrix.o
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeriesFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
     char inline1[1024];
          ^~~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
     int nmat;
         ^~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
     int n, llimit, ulimit;
         ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
     int n, llimit, ulimit;
            ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
     int n, llimit, ulimit;
                    ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1361:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (j = 0; j < curline.length(); j++) {
               ~~^~~~~~~~~~~~~~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])':
ClustalW/substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
     int maxRes;
         ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])':
ClustalW/substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
     int maxRes;
         ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1128:19: warning: 'n' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return (maxRes);
                   ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/ClusterTree.cpp -o ClustalW/tree/ClusterTree.o
ClustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
ClustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
     int rs = 0, rl = 0;
         ^~
ClustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
     int rs = 0, rl = 0;
                 ^~
ClustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::promptForBoolSeedAndNumTrials()':
ClustalW/tree/ClusterTree.cpp:967:22: warning: variable 'tempSeed' set but not used [-Wunused-but-set-variable]
         unsigned int tempSeed;
                      ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/UPGMA/Node.cpp -o ClustalW/tree/UPGMA/Node.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/UPGMA/RootedClusterTree.cpp -o ClustalW/tree/UPGMA/RootedClusterTree.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/UPGMA/RootedGuideTree.cpp -o ClustalW/tree/UPGMA/RootedGuideTree.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/UPGMA/RootedTreeOutput.cpp -o ClustalW/tree/UPGMA/RootedTreeOutput.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp -o ClustalW/tree/UPGMA/UPGMAAlgorithm.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/aligngivenpath.cpp -o Muscle/aligngivenpath.o
Muscle/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&)':
Muscle/aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
  const unsigned uLengthA = msaA.GetColCount();
                 ^~~~~~~~
Muscle/aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
  const unsigned uLengthB = msaB.GetColCount();
                 ^~~~~~~~
Muscle/aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
Muscle/aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^~~~~
Muscle/aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^~~~~
Muscle/aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^~~~~
Muscle/aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/aligngivenpath.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/aligngivenpathsw.cpp -o Muscle/aligngivenpathsw.o
Muscle/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&)':
Muscle/aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
  const unsigned uLengthA = msaA.GetColCount();
                 ^~~~~~~~
Muscle/aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
  const unsigned uLengthB = msaB.GetColCount();
                 ^~~~~~~~
Muscle/aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
Muscle/aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^~~~~
Muscle/aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^~~~~
Muscle/aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^~~~~
Muscle/aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/aligngivenpathsw.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/aligntwomsas.cpp -o Muscle/aligntwomsas.o
In file included from Muscle/aligntwomsas.cpp:6:
Muscle/timing.h:5: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/aligntwomsas.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/aligntwoprofs.cpp -o Muscle/aligntwoprofs.o
In file included from Muscle/muscle.h:37,
                 from Muscle/aligntwoprofs.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/aln.cpp -o Muscle/aln.o
In file included from Muscle/muscle.h:37,
                 from Muscle/aln.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/alpha.cpp -o Muscle/alpha.o
Muscle/alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)':
Muscle/alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  switch (Alpha)
         ^
In file included from Muscle/muscle.h:37,
                 from Muscle/alpha.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/anchors.cpp -o Muscle/anchors.o
Muscle/anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)':
Muscle/anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
    unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
             ^~~~~~~~~~~~~
Muscle/anchors.cpp: At global scope:
Muscle/anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
 static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
             ^~~~~~~~~~~~
Muscle/anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
 static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
             ^~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/anchors.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/bittraceback.cpp -o Muscle/bittraceback.o
Muscle/bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)':
Muscle/bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
  char Bits = TraceBack[uLengthA][uLengthB];
       ^~~~
Muscle/bittraceback.cpp: At global scope:
Muscle/bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
 static const char *BitsToStr(char Bits)
                    ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/bittraceback.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/blosum62.cpp -o Muscle/blosum62.o
In file included from Muscle/muscle.h:37,
                 from Muscle/blosum62.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/blosumla.cpp -o Muscle/blosumla.o
Muscle/blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
 static float Blosum62LA[20][20] =
              ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/blosumla.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/clust.cpp -o Muscle/clust.o
Muscle/clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)':
Muscle/clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  switch (m_JoinStyle)
         ^
Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
Muscle/clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
  const unsigned uClusterCount = GetClusterCount();
                 ^~~~~~~~~~~~~
Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
Muscle/clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
  const unsigned uClusterCount = GetClusterCount();
                 ^~~~~~~~~~~~~
Muscle/clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)':
Muscle/clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
  switch (m_CentroidStyle)
         ^
Muscle/clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
Muscle/clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
  const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
              ^~~~~~~
Muscle/clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const':
Muscle/clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  switch (m_JoinStyle)
         ^
In file included from Muscle/muscle.h:37,
                 from Muscle/clust.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/cluster.cpp -o Muscle/cluster.o
Muscle/cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
Muscle/cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
   bool bFound = false;
        ^~~~~~
Muscle/cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
  double dMaxDist = 0.0;
         ^~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/cluster.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
Muscle/cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wmaybe-uninitialized]
   ClusterNode &Child2 = m_Nodes[uIndexClosest2];
                                               ^
Muscle/cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   ClusterNode &Child1 = m_Nodes[uIndexClosest1];
                                               ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/clwwt.cpp -o Muscle/clwwt.o
In file included from Muscle/muscle.h:37,
                 from Muscle/clwwt.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/color.cpp -o Muscle/color.o
Muscle/color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
 static int BlosumScore(char c1, char c2)
            ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/color.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/cons.cpp -o Muscle/cons.o
In file included from Muscle/muscle.h:37,
                 from Muscle/cons.cpp:7:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/diaglist.cpp -o Muscle/diaglist.o
In file included from Muscle/muscle.h:37,
                 from Muscle/diaglist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
Muscle/diaglist.cpp:12:20: warning: 'uStartPosB' may be used uninitialized in this function [-Wmaybe-uninitialized]
  m_Diags[m_uCount] = d;
  ~~~~~~~~~~~~~~~~~~^~~
Muscle/diaglist.cpp:52:11: note: 'uStartPosB' was declared here
  unsigned uStartPosB;
           ^~~~~~~~~~
Muscle/diaglist.cpp:12:20: warning: 'uStartPosA' may be used uninitialized in this function [-Wmaybe-uninitialized]
  m_Diags[m_uCount] = d;
  ~~~~~~~~~~~~~~~~~~^~~
Muscle/diaglist.cpp:51:11: note: 'uStartPosA' was declared here
  unsigned uStartPosA;
           ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/diffobjscore.cpp -o Muscle/diffobjscore.o
Muscle/diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)':
Muscle/diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
  const unsigned uSeqCount = msa.GetSeqCount();
                 ^~~~~~~~~
Muscle/diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
  const unsigned uColCount = msa.GetColCount();
                 ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/diffobjscore.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/diffpaths.cpp -o Muscle/diffpaths.o
In file included from Muscle/muscle.h:37,
                 from Muscle/diffpaths.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/difftrees.cpp -o Muscle/difftrees.o
Muscle/difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)':
Muscle/difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
  const unsigned uLeafCount2 = Tree2.GetLeafCount();
                 ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/difftrees.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/difftreese.cpp -o Muscle/difftreese.o
In file included from Muscle/muscle.h:37,
                 from Muscle/difftreese.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/distcalc.cpp -o Muscle/distcalc.o
In file included from Muscle/muscle.h:37,
                 from Muscle/distcalc.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/distfunc.cpp -o Muscle/distfunc.o
In file included from Muscle/muscle.h:37,
                 from Muscle/distfunc.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/distpwkimura.cpp -o Muscle/distpwkimura.o
In file included from Muscle/muscle.h:37,
                 from Muscle/distpwkimura.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/domuscle.cpp -o Muscle/domuscle.o
In file included from Muscle/domuscle.cpp:9:
Muscle/timing.h:5: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 
Muscle/domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)':
Muscle/domuscle.cpp:169:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (g_bClusterOnly)
   ^~
Muscle/domuscle.cpp:172:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    return;
    ^~~~~~
Muscle/domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable]
  int PNlength = (msaInput->inputSeqs).Length();
      ^~~~~~~~
In file included from Muscle/domuscle.cpp:9:
Muscle/timing.h: At global scope:
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^~~~~~~~~~~
In file included from ./Muscle/muscle.h:37,
                 from ./RMuscle.h:4,
                 from Muscle/domuscle.cpp:1:
./Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/dosp.cpp -o Muscle/dosp.o
In file included from Muscle/muscle.h:37,
                 from Muscle/dosp.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/dpreglist.cpp -o Muscle/dpreglist.o
Muscle/dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)':
Muscle/dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
    const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
                   ^~~~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/dpreglist.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/drawtree.cpp -o Muscle/drawtree.o
In file included from Muscle/muscle.h:37,
                 from Muscle/drawtree.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/edgelist.cpp -o Muscle/edgelist.o
In file included from Muscle/muscle.h:37,
                 from Muscle/edgelist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/enumopts.cpp -o Muscle/enumopts.o
In file included from Muscle/muscle.h:37,
                 from Muscle/enumopts.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/enumtostr.cpp -o Muscle/enumtostr.o
In file included from Muscle/muscle.h:37,
                 from Muscle/enumtostr.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/estring.cpp -o Muscle/estring.o
Muscle/estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
 static bool CanMultiplyEstrings(const short es1[], const short es2[])
             ^~~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/estring.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)':
Muscle/estring.cpp:424:14: warning: 'cType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   Edge.cType = cType;
   ~~~~~~~~~~~^~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fasta.cpp -o Muscle/fasta.o
Muscle/fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)':
Muscle/fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
  unsigned uSeqCount = 0;
           ^~~~~~~~~
Muscle/fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
  unsigned uColCount = uInsane;
           ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/fasta.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fasta2.cpp -o Muscle/fasta2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fasta2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fastclust.cpp -o Muscle/fastclust.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastclust.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fastdist.cpp -o Muscle/fastdist.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fastdistjones.cpp -o Muscle/fastdistjones.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistjones.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fastdistkbit.cpp -o Muscle/fastdistkbit.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistkbit.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fastdistkmer.cpp -o Muscle/fastdistkmer.o
Muscle/fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)':
Muscle/fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
    double KD = KimuraDist(EstimatedPctId);
           ^~
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistkmer.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fastdistmafft.cpp -o Muscle/fastdistmafft.o
Muscle/fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
Muscle/fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable]
   const char *pName1 = s1.GetName();
               ^~~~~~
Muscle/fastdistmafft.cpp: At global scope:
Muscle/fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
 static void ListCount(const unsigned char Count[])
             ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistmafft.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fastdistnuc.cpp -o Muscle/fastdistnuc.o
Muscle/fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)':
Muscle/fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
   const char *pName1 = s1.GetName();
               ^~~~~~
Muscle/fastdistnuc.cpp: At global scope:
Muscle/fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
 static void ListCount(const unsigned char Count[])
             ^~~~~~~~~
Muscle/fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
 static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
                 ^~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistnuc.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/fastscorepath2.cpp -o Muscle/fastscorepath2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastscorepath2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/finddiags.cpp -o Muscle/finddiags.o
Muscle/finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
 static char *TupleToStr(int t)
              ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/finddiags.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/finddiagsn.cpp -o Muscle/finddiagsn.o
Muscle/finddiagsn.cpp: In function 'char* TupleToStr(int)':
Muscle/finddiagsn.cpp:16:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  for (int i = 0; i < K; ++i)
                  ~~^~~
Muscle/finddiagsn.cpp: At global scope:
Muscle/finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
 static char *TupleToStr(int t)
              ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/finddiagsn.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalign.cpp -o Muscle/glbalign.o
In file included from Muscle/glbalign.cpp:3:
Muscle/timing.h:5: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalign.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalign352.cpp -o Muscle/glbalign352.o
In file included from Muscle/glbalign352.cpp:3:
Muscle/timing.h:5: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalign352.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbaligndiag.cpp -o Muscle/glbaligndiag.o
In file included from Muscle/glbaligndiag.cpp:6:
Muscle/timing.h:5: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbaligndiag.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalignla.cpp -o Muscle/glbalignla.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignla.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/glbalignla.cpp: In function 'SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignla.cpp:427:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                ^~~~~~~~~~~~~~~~
Muscle/glbalignla.cpp:366:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                        ^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalignle.cpp -o Muscle/glbalignle.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignle.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignle.cpp:431:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                ^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalignns.cpp -o Muscle/glbalignns.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignns.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/glbalignns.cpp: In function 'SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignns.cpp:366:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                ^~~~~~~~~~~~~~~~
Muscle/glbalignns.cpp:305:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                        ^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalignsimple.cpp -o Muscle/glbalignsimple.o
Muscle/glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
             ^~~~~~
Muscle/glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
             ^~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignsimple.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalignsp.cpp -o Muscle/glbalignsp.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignsp.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignsp.cpp:366:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                ^~~~~~~~~~~~~~~~
Muscle/glbalignsp.cpp:305:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                        ^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalignspn.cpp -o Muscle/glbalignspn.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignspn.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignspn.cpp:401:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                ^~~~~~~~~~~~~~~~
Muscle/glbalignspn.cpp:340:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                        ^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalignss.cpp -o Muscle/glbalignss.o
Muscle/glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
Muscle/glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
   const SCORE *ptrRowA = MxRowA[i];
                ^~~~~~~
Muscle/glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
  const unsigned uPrefixCountA = uLengthA + 1;
                 ^~~~~~~~~~~~~
Muscle/glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^~~~~~~~~~~~~
Muscle/glbalignss.cpp: At global scope:
Muscle/glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
              ^~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignss.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
Muscle/glbalignss.cpp:310:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                ^~~~~~~~~~~~~~~~
Muscle/glbalignss.cpp:252:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                        ^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/glbalndimer.cpp -o Muscle/glbalndimer.o
Muscle/glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)':
Muscle/glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  switch (g_PPScore)
         ^
Muscle/glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
Muscle/glbalndimer.cpp: At global scope:
Muscle/glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
 static const char *LocalScoreToStr(SCORE s)
                    ^~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalndimer.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/globals.cpp -o Muscle/globals.o
In file included from Muscle/muscle.h:37,
                 from Muscle/globals.cpp:6:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/globalslinux.cpp -o Muscle/globalslinux.o
In file included from Muscle/muscle.h:37,
                 from Muscle/globalslinux.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/globalsosx.cpp -o Muscle/globalsosx.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/globalsother.cpp -o Muscle/globalsother.o
In file included from Muscle/muscle.h:37,
                 from Muscle/globalsother.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/globalswin32.cpp -o Muscle/globalswin32.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/gonnet.cpp -o Muscle/gonnet.o
Muscle/gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
 static SCORE Gonnet160[20][20] =
              ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/gonnet.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/gotowt.cpp -o Muscle/gotowt.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/henikoffweight.cpp -o Muscle/henikoffweight.o
In file included from Muscle/muscle.h:37,
                 from Muscle/henikoffweight.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/henikoffweightpb.cpp -o Muscle/henikoffweightpb.o
In file included from Muscle/muscle.h:37,
                 from Muscle/henikoffweightpb.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/html.cpp -o Muscle/html.o
In file included from Muscle/muscle.h:37,
                 from Muscle/html.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/hydro.cpp -o Muscle/hydro.o
In file included from Muscle/muscle.h:37,
                 from Muscle/hydro.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/intmath.cpp -o Muscle/intmath.o
In file included from Muscle/muscle.h:37,
                 from Muscle/intmath.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/local.cpp -o Muscle/local.o
In file included from Muscle/muscle.h:37,
                 from Muscle/local.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/main.cpp -o Muscle/main.o
In file included from Muscle/muscle.h:37,
                 from Muscle/main.cpp:3:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/makerootmsa.cpp -o Muscle/makerootmsa.o
Muscle/makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)':
Muscle/makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
  const unsigned uSeqLength = s.Length();
                 ^~~~~~~~~~
Muscle/makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
Muscle/makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
   const PWPath &Path = Nodes[uNodeIndex].m_Path;
                 ^~~~
Muscle/makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
Muscle/makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
  const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
                 ^~~~~~~~~~~~~~
Muscle/makerootmsa.cpp: At global scope:
Muscle/makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
 static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
             ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/makerootmsa.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/makerootmsab.cpp -o Muscle/makerootmsab.o
In file included from Muscle/muscle.h:37,
                 from Muscle/makerootmsab.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/maketree.cpp -o Muscle/maketree.o
In file included from Muscle/muscle.h:37,
                 from Muscle/maketree.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/mhack.cpp -o Muscle/mhack.o
In file included from Muscle/muscle.h:37,
                 from Muscle/mhack.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/mpam200.cpp -o Muscle/mpam200.o
In file included from Muscle/muscle.h:37,
                 from Muscle/mpam200.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/msa.cpp -o Muscle/msa.o
Muscle/msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
 static void FmtPad(unsigned n)
             ^~~~~~
Muscle/msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void FmtInt0(unsigned u, unsigned uWidth)
             ^~~~~~~
Muscle/msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void FmtInt(unsigned u, unsigned uWidth)
             ^~~~~~
Muscle/msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
 static void FmtChar(char c, unsigned uWidth)
             ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/msa.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/msa2.cpp -o Muscle/msa2.o
Muscle/msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)':
Muscle/msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
  switch (Method)
         ^
Muscle/msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
Muscle/msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
  const unsigned uColCountCat = uColCount1 + uColCount2;
                 ^~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/msa2.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/msadistkimura.cpp -o Muscle/msadistkimura.o
In file included from Muscle/muscle.h:37,
                 from Muscle/msadistkimura.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/msf.cpp -o Muscle/msf.o
Muscle/msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
 static const char *strfind(const char *s, const char *t)
                    ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/msf.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/muscle.cpp -o Muscle/muscle.o
In file included from Muscle/muscle.h:37,
                 from Muscle/muscle.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/muscleout.cpp -o Muscle/muscleout.o
In file included from Muscle/muscle.h:37,
                 from Muscle/muscleout.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/nucmx.cpp -o Muscle/nucmx.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nucmx.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/nwdasimple.cpp -o Muscle/nwdasimple.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nwdasimple.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/nwdasimple2.cpp -o Muscle/nwdasimple2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nwdasimple2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/nwdasmall.cpp -o Muscle/nwdasmall.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nwdasmall.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/nwrec.cpp -o Muscle/nwrec.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/nwsmall.cpp -o Muscle/nwsmall.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nwsmall.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/objscore.cpp -o Muscle/objscore.o
In file included from Muscle/objscore.cpp:5:
Muscle/timing.h:5: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 
Muscle/objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)':
Muscle/objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch]
  switch (OS)
         ^
Muscle/objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
In file included from Muscle/objscore.cpp:5:
Muscle/timing.h: At global scope:
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/objscore.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/objscore2.cpp -o Muscle/objscore2.o
Muscle/objscore2.cpp: In function 'SCORE TermGapScore(bool)':
Muscle/objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
  switch (g_TermGaps)
         ^
Muscle/objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
Muscle/objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
  SCORE scoreGaps = 0;
        ^~~~~~~~~
Muscle/objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
  bool bGapping1 = false;
       ^~~~~~~~~
Muscle/objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
  bool bGapping2 = false;
       ^~~~~~~~~
Muscle/objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
  bool bLeftTermGap = false;
       ^~~~~~~~~~~~
Muscle/objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
  bool bRightTermGap = false;
       ^~~~~~~~~~~~~
Muscle/objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)':
Muscle/objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
  bool bLeftTermGap = false;
       ^~~~~~~~~~~~
Muscle/objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
  bool bRightTermGap = false;
       ^~~~~~~~~~~~~
Muscle/objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
Muscle/objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
  const unsigned uColCount2 = msa2.GetColCount();
                 ^~~~~~~~~~
Muscle/objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
Muscle/objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
    const WEIGHT w = w1*w2;
                 ^
In file included from Muscle/muscle.h:37,
                 from Muscle/objscore2.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/objscoreda.cpp -o Muscle/objscoreda.o
In file included from Muscle/muscle.h:37,
                 from Muscle/objscoreda.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/onexception.cpp -o Muscle/onexception.o
In file included from Muscle/muscle.h:37,
                 from Muscle/onexception.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/options.cpp -o Muscle/options.o
In file included from Muscle/muscle.h:37,
                 from Muscle/options.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/outweights.cpp -o Muscle/outweights.o
In file included from Muscle/muscle.h:37,
                 from Muscle/outweights.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/pam200mafft.cpp -o Muscle/pam200mafft.o
Muscle/pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
 static float PAM200[23][23] =
              ^~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/pam200mafft.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/params.cpp -o Muscle/params.o
Muscle/params.cpp: In function 'void SetPPScore(bool)':
Muscle/params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  switch (g_PPScore)
         ^
In file included from Muscle/muscle.h:37,
                 from Muscle/params.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/phy.cpp -o Muscle/phy.o
Muscle/phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)':
Muscle/phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
  double dEdgeLength = GetEdgeLength(uNode1, uNode2);
         ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/phy.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/phy2.cpp -o Muscle/phy2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phy2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/phy3.cpp -o Muscle/phy3.o
Muscle/phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)':
Muscle/phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
  const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
               ^~~~~~~~~
Muscle/phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
Muscle/phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
  const unsigned uLeafCount = tree.GetLeafCount();
                 ^~~~~~~~~~
Muscle/phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
  double dAllMaxDist = -1e20;
         ^~~~~~~~~~~
Muscle/phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
  unsigned uMaxFrom = NULL_NEIGHBOR;
           ^~~~~~~~
Muscle/phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
  unsigned uMaxTo = NULL_NEIGHBOR;
           ^~~~~~
Muscle/phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)':
Muscle/phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
  unsigned uMostDistantLeaf = NULL_NEIGHBOR;
           ^~~~~~~~~~~~~~~~
Muscle/phy3.cpp: At global scope:
Muscle/phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
 static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
             ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/phy3.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/phy4.cpp -o Muscle/phy4.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phy4.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/phyfromclust.cpp -o Muscle/phyfromclust.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phyfromclust.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/phyfromfile.cpp -o Muscle/phyfromfile.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phyfromfile.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/physeq.cpp -o Muscle/physeq.o
Muscle/physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
Muscle/physeq.cpp:60:13: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     if (Col == ColCount)
         ~~~~^~~~~~~~~~~
Muscle/physeq.cpp:71:12: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
    if (Col == ColCount)
        ~~~~^~~~~~~~~~~
Muscle/physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
Muscle/physeq.cpp:112:13: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     if (Col == ColCount)
         ~~~~^~~~~~~~~~~
Muscle/physeq.cpp:124:11: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   if (Col == ColCount)
       ~~~~^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/physeq.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/phytofile.cpp -o Muscle/phytofile.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phytofile.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/posgap.cpp -o Muscle/posgap.o
In file included from Muscle/muscle.h:37,
                 from Muscle/posgap.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/ppscore.cpp -o Muscle/ppscore.o
In file included from Muscle/muscle.h:37,
                 from Muscle/ppscore.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/profdb.cpp -o Muscle/profdb.o
In file included from Muscle/clustsetmsa.h:8,
                 from Muscle/profdb.cpp:9:
Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
   switch(m_Distance)
         ^
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
In file included from Muscle/muscle.h:37,
                 from Muscle/profdb.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/profile.cpp -o Muscle/profile.o
In file included from Muscle/muscle.h:37,
                 from Muscle/profile.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/profilefrommsa.cpp -o Muscle/profilefrommsa.o
Muscle/profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)':
Muscle/profilefrommsa.cpp:131:10: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   if (-1 == PP.m_uResidueGroup)
       ~~~^~~~~~~~~~~~~~~~~~~~~
Muscle/profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)':
Muscle/profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  switch (g_Alpha)
         ^
Muscle/profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
Muscle/profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
  const unsigned uSeqCount = a.GetSeqCount();
                 ^~~~~~~~~
Muscle/profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
  unsigned uHydrophobicRunLength = 0;
           ^~~~~~~~~~~~~~~~~~~~~
Muscle/profilefrommsa.cpp: At global scope:
Muscle/profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
 static const char *LocalScoreToStr(SCORE s)
                    ^~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/profilefrommsa.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/progalign.cpp -o Muscle/progalign.o
Muscle/progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)':
Muscle/progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
  const unsigned uIterCount = uSeqCount - 1;
                 ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/progalign.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/progress.cpp -o Muscle/progress.o
In file included from Muscle/muscle.h:37,
                 from Muscle/progress.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/progressivealign.cpp -o Muscle/progressivealign.o
In file included from Muscle/muscle.h:37,
                 from Muscle/progressivealign.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/pwpath.cpp -o Muscle/pwpath.o
Muscle/pwpath.cpp: In member function 'void PWPath::Validate() const':
Muscle/pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable]
  const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
                ^~~~~~~~
Muscle/pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
Muscle/pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
  unsigned uEdgeIndex = 0;
           ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/pwpath.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/readmx.cpp -o Muscle/readmx.o
Muscle/readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
Muscle/readmx.cpp:83:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  for (int i = 0; i < MAX_ALPHA; ++i)
                  ~~^~~~~~~~~~~
Muscle/readmx.cpp:84:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for (int j = 0; j < MAX_ALPHA; ++j)
                   ~~^~~~~~~~~~~
Muscle/readmx.cpp: In function 'float (* ReadMxFromR(std::vector<std::__cxx11::basic_string<char> >, float (*)[32]))[32][32]':
Muscle/readmx.cpp:184:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  for (int i = 0; i < MAX_ALPHA; ++i)
                  ~~^~~~~~~~~~~
Muscle/readmx.cpp:185:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for (int j = 0; j < MAX_ALPHA; ++j)
                   ~~^~~~~~~~~~~
Muscle/readmx.cpp: At global scope:
Muscle/readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
 static unsigned MxCharToLetter(char c)
                 ^~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/readmx.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/realigndiffs.cpp -o Muscle/realigndiffs.o
In file included from Muscle/muscle.h:37,
                 from Muscle/realigndiffs.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/realigndiffse.cpp -o Muscle/realigndiffse.o
Muscle/realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)':
Muscle/realigndiffse.cpp:77:13: warning: unused variable 'uNewRight' [-Wunused-variable]
    unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
             ^~~~~~~~~
Muscle/realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable]
    unsigned uOldRight = OldTree.GetRight(uOld);
             ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/realigndiffse.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/refine.cpp -o Muscle/refine.o
In file included from Muscle/clustsetmsa.h:8,
                 from Muscle/refine.cpp:9:
Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
   switch(m_Distance)
         ^
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
In file included from Muscle/muscle.h:37,
                 from Muscle/refine.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/refinehoriz.cpp -o Muscle/refinehoriz.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refinehoriz.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/refinesubfams.cpp -o Muscle/refinesubfams.o
Muscle/refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)':
Muscle/refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
  const unsigned uNodeCount = tree.GetNodeCount();
                 ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/refinesubfams.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/refinetree.cpp -o Muscle/refinetree.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refinetree.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/refinetreee.cpp -o Muscle/refinetreee.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refinetreee.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/refinevert.cpp -o Muscle/refinevert.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refinevert.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/refinew.cpp -o Muscle/refinew.o
Muscle/refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
Muscle/refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
  const unsigned uColCountCat = uColCount1 + uColCount2;
                 ^~~~~~~~~~~~
Muscle/refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
Muscle/refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable]
    unsigned uOutCols = msaOut.GetColCount();
             ^~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/refinew.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/savebest.cpp -o Muscle/savebest.o
In file included from Muscle/muscle.h:37,
                 from Muscle/savebest.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/scoredist.cpp -o Muscle/scoredist.o
In file included from Muscle/muscle.h:37,
                 from Muscle/scoredist.cpp:3:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/scoregaps.cpp -o Muscle/scoregaps.o
Muscle/scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
 static SCORE Penalty(unsigned Length, bool Term)
              ^~~~~~~
Muscle/scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
 static void FreeGapInfo(GAPINFO *GI)
             ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/scoregaps.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/scorehistory.cpp -o Muscle/scorehistory.o
In file included from Muscle/muscle.h:37,
                 from Muscle/scorehistory.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/scorepp.cpp -o Muscle/scorepp.o
In file included from Muscle/muscle.h:37,
                 from Muscle/scorepp.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/seq.cpp -o Muscle/seq.o
In file included from Muscle/muscle.h:37,
                 from Muscle/seq.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/seqvect.cpp -o Muscle/seqvect.o
In file included from Muscle/muscle.h:37,
                 from Muscle/seqvect.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/setblosumweights.cpp -o Muscle/setblosumweights.o
In file included from Muscle/muscle.h:37,
                 from Muscle/setblosumweights.cpp:42:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/setgscweights.cpp -o Muscle/setgscweights.o
In file included from Muscle/muscle.h:37,
                 from Muscle/setgscweights.cpp:104:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/setnewhandler.cpp -o Muscle/setnewhandler.o
In file included from Muscle/muscle.h:37,
                 from Muscle/setnewhandler.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/spfast.cpp -o Muscle/spfast.o
Muscle/spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)':
Muscle/spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
  const unsigned uSeqCount = msa.GetSeqCount();
                 ^~~~~~~~~
Muscle/spfast.cpp: At global scope:
Muscle/spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
 static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
              ^~~~~~~~~~
Muscle/spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
 static const char *GapTypeToStr(int GapType)
                    ^~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/spfast.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/sptest.cpp -o Muscle/sptest.o
In file included from Muscle/muscle.h:37,
                 from Muscle/sptest.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/stabilize.cpp -o Muscle/stabilize.o
In file included from Muscle/muscle.h:37,
                 from Muscle/stabilize.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/subfam.cpp -o Muscle/subfam.o
Muscle/subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)':
Muscle/subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
  int NotUsed = system(CmdLine);
      ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/subfam.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/subfams.cpp -o Muscle/subfams.o
Muscle/subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void Relax(DistFunc &DF, unsigned u, unsigned v)
             ^~~~~
Muscle/subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
 static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
             ^~~~~~~~~~~~~~~~~~~~~~
Muscle/subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
 static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
             ^~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/subfams.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/sw.cpp -o Muscle/sw.o
Muscle/sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
             ^~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/sw.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/termgaps.cpp -o Muscle/termgaps.o
In file included from Muscle/muscle.h:37,
                 from Muscle/termgaps.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/textfile.cpp -o Muscle/textfile.o
Muscle/textfile.cpp: In member function 'void TextFile::PutChar(char)':
Muscle/textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fputc(c, m_ptrFile);
      ^
Muscle/textfile.cpp: In member function 'void TextFile::PutString(const char*)':
Muscle/textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable]
  int iError = fputs(szLine, m_ptrFile);
      ^~~~~~
Muscle/textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
Muscle/textfile.cpp:224:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fgetpos(m_ptrFile, &p);
      ^
Muscle/textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
Muscle/textfile.cpp:237:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fsetpos(m_ptrFile, &p);
      ^
In file included from Muscle/muscle.h:37,
                 from Muscle/textfile.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/threewaywt.cpp -o Muscle/threewaywt.o
In file included from Muscle/muscle.h:37,
                 from Muscle/threewaywt.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/tomhydro.cpp -o Muscle/tomhydro.o
In file included from Muscle/muscle.h:37,
                 from Muscle/tomhydro.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/traceback.cpp -o Muscle/traceback.o
Muscle/traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)':
Muscle/traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/traceback.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)':
Muscle/traceback.cpp:72:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   switch (cEdgeType)
   ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/tracebackopt.cpp -o Muscle/tracebackopt.o
In file included from Muscle/muscle.h:37,
                 from Muscle/tracebackopt.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/tracebacksw.cpp -o Muscle/tracebacksw.o
Muscle/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&)':
Muscle/tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
  SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
        ^~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/tracebacksw.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/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&)':
Muscle/tracebacksw.cpp:47:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   switch (cEdgeType)
   ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/treefrommsa.cpp -o Muscle/treefrommsa.o
In file included from Muscle/clustsetmsa.h:8,
                 from Muscle/treefrommsa.cpp:5:
Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
   switch(m_Distance)
         ^
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
In file included from Muscle/muscle.h:37,
                 from Muscle/treefrommsa.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/typetostr.cpp -o Muscle/typetostr.o
In file included from Muscle/muscle.h:37,
                 from Muscle/typetostr.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/upgma2.cpp -o Muscle/upgma2.o
Muscle/upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
 static void ListState()
             ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/upgma2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
Muscle/upgma2.cpp:292:15: warning: 'dtNewDist' may be used uninitialized in this function [-Wmaybe-uninitialized]
    g_Dist[vL] = dtNewDist;
    ~~~~~~~~~~~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/usage.cpp -o Muscle/usage.o
In file included from Muscle/muscle.h:37,
                 from Muscle/usage.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/validateids.cpp -o Muscle/validateids.o
In file included from Muscle/muscle.h:37,
                 from Muscle/validateids.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/vtml2.cpp -o Muscle/vtml2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/vtml2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Muscle/writescorefile.cpp -o Muscle/writescorefile.o
In file included from Muscle/muscle.h:37,
                 from Muscle/writescorefile.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
Muscle/writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)':
Muscle/writescorefile.cpp:40:9: warning: 'Score' may be used uninitialized in this function [-Wmaybe-uninitialized]
    dSum += Score;
    ~~~~~^~~~~~~~
Muscle/writescorefile.cpp:27:11: note: 'Score' was declared here
    double Score;
           ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RClustalW.cpp -o RClustalW.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RClustalWMain.cpp -o RClustalWMain.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RMuscle.cpp -o RMuscle.o
In file included from Muscle/muscle.h:37,
                 from RMuscle.h:4,
                 from RMuscle.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o enhancerHomologSearch.dll tmp.def ClustalW/alignment/Alignment.o ClustalW/alignment/AlignmentOutput.o ClustalW/alignment/ObjectiveScore.o ClustalW/alignment/Sequence.o ClustalW/Clustal.o ClustalW/fileInput/ClustalFileParser.o ClustalW/fileInput/EMBLFileParser.o ClustalW/fileInput/FileParser.o ClustalW/fileInput/FileReader.o ClustalW/fileInput/GDEFileParser.o ClustalW/fileInput/InFileStream.o ClustalW/fileInput/MSFFileParser.o ClustalW/fileInput/PearsonFileParser.o ClustalW/fileInput/PIRFileParser.o ClustalW/fileInput/RSFFileParser.o ClustalW/general/ClustalWResources.o ClustalW/general/DebugLog.o ClustalW/general/InvalidCombination.o ClustalW/general/OutputFile.o ClustalW/general/Stats.o ClustalW/general/SymMatrix.o ClustalW/general/UserParameters.o ClustalW/general/Utility.o ClustalW/general/VectorOutOfRange.o ClustalW/Help.o ClustalW/interface/CommandLineParser.o ClustalW/multipleAlign/Iteration.o ClustalW/multipleAlign/LowScoreSegProfile.o ClustalW/multipleAlign/MSA.o ClustalW/multipleAlign/MyersMillerProfileAlign.o ClustalW/multipleAlign/ProfileBase.o ClustalW/multipleAlign/ProfileStandard.o ClustalW/multipleAlign/ProfileWithSub.o ClustalW/pairwise/FastPairwiseAlign.o ClustalW/pairwise/FullPairwiseAlign.o ClustalW/substitutionMatrix/SubMatrix.o ClustalW/tree/AlignmentSteps.o ClustalW/tree/ClusterTree.o ClustalW/tree/ClusterTreeOutput.o ClustalW/tree/NJTree.o ClustalW/tree/RandomGenerator.o ClustalW/tree/Tree.o ClustalW/tree/TreeInterface.o ClustalW/tree/UnRootedClusterTree.o ClustalW/tree/UPGMA/Node.o ClustalW/tree/UPGMA/RootedClusterTree.o ClustalW/tree/UPGMA/RootedGuideTree.o ClustalW/tree/UPGMA/RootedTreeOutput.o ClustalW/tree/UPGMA/UPGMAAlgorithm.o Muscle/aligngivenpath.o Muscle/aligngivenpathsw.o Muscle/aligntwomsas.o Muscle/aligntwoprofs.o Muscle/aln.o Muscle/alpha.o Muscle/anchors.o Muscle/bittraceback.o Muscle/blosum62.o Muscle/blosumla.o Muscle/clust.o Muscle/cluster.o Muscle/clwwt.o Muscle/color.o Muscle/cons.o Muscle/diaglist.o Muscle/diffobjscore.o Muscle/diffpaths.o Muscle/difftrees.o Muscle/difftreese.o Muscle/distcalc.o Muscle/distfunc.o Muscle/distpwkimura.o Muscle/domuscle.o Muscle/dosp.o Muscle/dpreglist.o Muscle/drawtree.o Muscle/edgelist.o Muscle/enumopts.o Muscle/enumtostr.o Muscle/estring.o Muscle/fasta.o Muscle/fasta2.o Muscle/fastclust.o Muscle/fastdist.o Muscle/fastdistjones.o Muscle/fastdistkbit.o Muscle/fastdistkmer.o Muscle/fastdistmafft.o Muscle/fastdistnuc.o Muscle/fastscorepath2.o Muscle/finddiags.o Muscle/finddiagsn.o Muscle/glbalign.o Muscle/glbalign352.o Muscle/glbaligndiag.o Muscle/glbalignla.o Muscle/glbalignle.o Muscle/glbalignns.o Muscle/glbalignsimple.o Muscle/glbalignsp.o Muscle/glbalignspn.o Muscle/glbalignss.o Muscle/glbalndimer.o Muscle/globals.o Muscle/globalslinux.o Muscle/globalsosx.o Muscle/globalsother.o Muscle/globalswin32.o Muscle/gonnet.o Muscle/gotowt.o Muscle/henikoffweight.o Muscle/henikoffweightpb.o Muscle/html.o Muscle/hydro.o Muscle/intmath.o Muscle/local.o Muscle/main.o Muscle/makerootmsa.o Muscle/makerootmsab.o Muscle/maketree.o Muscle/mhack.o Muscle/mpam200.o Muscle/msa.o Muscle/msa2.o Muscle/msadistkimura.o Muscle/msf.o Muscle/muscle.o Muscle/muscleout.o Muscle/nucmx.o Muscle/nwdasimple.o Muscle/nwdasimple2.o Muscle/nwdasmall.o Muscle/nwrec.o Muscle/nwsmall.o Muscle/objscore.o Muscle/objscore2.o Muscle/objscoreda.o Muscle/onexception.o Muscle/options.o Muscle/outweights.o Muscle/pam200mafft.o Muscle/params.o Muscle/phy.o Muscle/phy2.o Muscle/phy3.o Muscle/phy4.o Muscle/phyfromclust.o Muscle/phyfromfile.o Muscle/physeq.o Muscle/phytofile.o Muscle/posgap.o Muscle/ppscore.o Muscle/profdb.o Muscle/profile.o Muscle/profilefrommsa.o Muscle/progalign.o Muscle/progress.o Muscle/progressivealign.o Muscle/pwpath.o Muscle/readmx.o Muscle/realigndiffs.o Muscle/realigndiffse.o Muscle/refine.o Muscle/refinehoriz.o Muscle/refinesubfams.o Muscle/refinetree.o Muscle/refinetreee.o Muscle/refinevert.o Muscle/refinew.o Muscle/savebest.o Muscle/scoredist.o Muscle/scoregaps.o Muscle/scorehistory.o Muscle/scorepp.o Muscle/seq.o Muscle/seqvect.o Muscle/setblosumweights.o Muscle/setgscweights.o Muscle/setnewhandler.o Muscle/spfast.o Muscle/sptest.o Muscle/stabilize.o Muscle/subfam.o Muscle/subfams.o Muscle/sw.o Muscle/termgaps.o Muscle/textfile.o Muscle/threewaywt.o Muscle/tomhydro.o Muscle/traceback.o Muscle/tracebackopt.o Muscle/tracebacksw.o Muscle/treefrommsa.o Muscle/typetostr.o Muscle/upgma2.o Muscle/usage.o Muscle/validateids.o Muscle/vtml2.o Muscle/writescorefile.o RClustalW.o RClustalWMain.o RcppExports.o RMuscle.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-enhancerHomologSearch/00new/enhancerHomologSearch/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'enhancerHomologSearch'
    finding HTML links ... done
    Enhancers-class                         html  
    alignment                               html  
    alignmentOne                            html  
    conservedMotifs                         html  
    getENCODEdata                           html  
    motifs                                  html  
    queryEncode                             html  
    saveAlignments                          html  
    searchTFBPS                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (enhancerHomologSearch)
Making 'packages.html' ... done

Tests output

enhancerHomologSearch.Rcheck/tests/runTests.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("enhancerHomologSearch") || stop("unable to load Package:enhancerHomologSearch")
Loading required package: enhancerHomologSearch

[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg38") || stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg38")
Loading required package: BSgenome.Hsapiens.UCSC.hg38
Loading required package: BSgenome
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
[1] TRUE
> require("BSgenome.Mmusculus.UCSC.mm10") || stop("unable to load Package:BSgenome.Mmusculus.UCSC.mm10")
Loading required package: BSgenome.Mmusculus.UCSC.mm10
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
Loading required package: GenomicFeatures
[1] TRUE
> require("BiocParallel") || stop("unable to load BiocParallel")
Loading required package: BiocParallel
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("enhancerHomologSearch")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 361.90   48.17  431.59 

Example timings

enhancerHomologSearch.Rcheck/enhancerHomologSearch-Ex.timings

nameusersystemelapsed
Enhancers-class0.040.000.05
alignment3.100.173.26
alignmentOne4.110.144.25
conservedMotifs179.30 29.71209.73
getENCODEdata3.880.366.29
motifs0.160.030.19
queryEncode0.430.051.70
saveAlignments8.030.128.16
searchTFBPS266.19 37.70304.09