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CHECK report for muscle on veracruz1

This page was generated on 2018-04-12 13:40:24 -0400 (Thu, 12 Apr 2018).

Package 917/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
muscle 3.20.0
Alex T. Kalinka
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/muscle
Branch: RELEASE_3_6
Last Commit: dd09ffa
Last Changed Date: 2017-10-30 12:40:49 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: muscle
Version: 3.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings muscle_3.20.0.tar.gz
StartedAt: 2018-04-12 06:55:56 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 06:57:53 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 117.1 seconds
RetCode: 0
Status:  OK 
CheckDir: muscle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings muscle_3.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/muscle.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘muscle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘muscle’ version ‘3.20.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘muscle’ can be installed ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: OK


Installation output

muscle.Rcheck/00install.out

* installing *source* package ‘muscle’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c aligngivenpath.cpp -o aligngivenpath.o
aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
        const unsigned uLengthA = msaA.GetColCount();
                       ^
aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
        const unsigned uLengthB = msaB.GetColCount();
                       ^
aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
                        const unsigned uColA = uPrefixLengthA - 1;
                                       ^
aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
                        const unsigned uColB = uPrefixLengthB - 1;
                                       ^
aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
                        const unsigned uColA = uPrefixLengthA - 1;
                                       ^
aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
                        const unsigned uColB = uPrefixLengthB - 1;
                                       ^
In file included from aligngivenpath.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
7 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c aligngivenpathsw.cpp -o aligngivenpathsw.o
aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
        const unsigned uLengthB = msaB.GetColCount();
                       ^
aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
        const unsigned uLengthA = msaA.GetColCount();
                       ^
aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
                        const unsigned uColA = uPrefixLengthA - 1;
                                       ^
aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
                        const unsigned uColB = uPrefixLengthB - 1;
                                       ^
aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
                        const unsigned uColA = uPrefixLengthA - 1;
                                       ^
aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
                        const unsigned uColB = uPrefixLengthB - 1;
                                       ^
In file included from aligngivenpathsw.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
7 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c aligntwomsas.cpp -o aligntwomsas.o
In file included from aligntwomsas.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c aligntwoprofs.cpp -o aligntwoprofs.o
In file included from aligntwoprofs.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c aln.cpp -o aln.o
In file included from aln.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c alpha.cpp -o alpha.o
alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
        switch (Alpha)
                ^
In file included from alpha.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c anchors.cpp -o anchors.o
anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
                        unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
                                 ^
In file included from anchors.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function]
static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
            ^
anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function]
static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
            ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
        char Bits = TraceBack[uLengthA][uLengthB];
             ^
In file included from bittraceback.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function]
static const char *BitsToStr(char Bits)
                   ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c blosum62.cpp -o blosum62.o
In file included from blosum62.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c blosumla.cpp -o blosumla.o
In file included from blosumla.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable]
static float Blosum62LA[20][20] =
             ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c clust.cpp -o clust.o
clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
        switch (m_JoinStyle)
                ^
clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
        const unsigned uClusterCount = GetClusterCount();
                       ^
clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
        const unsigned uClusterCount = GetClusterCount();
                       ^
clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
        switch (m_CentroidStyle)
                ^
clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
        const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
                    ^
clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
        switch (m_JoinStyle)
                ^
In file included from clust.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
7 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cluster.cpp -o cluster.o
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
        double dMaxDist = 0.0;
               ^
In file included from cluster.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function]
static inline float Max(float d1, float d2)
                    ^
cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function]
static inline float Mean(float d1, float d2)
                    ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c clwwt.cpp -o clwwt.o
In file included from clwwt.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c color.cpp -o color.o
color.cpp:7:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +4, -2, +0, -2, -1,  -2, +0, -2, -1, -1,  -1, -1, -2, -1, -1,  -1, +1, +0, +0, -3,  -1, -2, -1,  // A
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:8:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, +6, -3, +6, +2,  -3, -1, -1, -3, -1,  -4, -3, +1, -1, +0,  -2, +0, -1, -3, -4,  -1, -3, +2,  // B
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:9:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +0, -3, +9, -3, -4,  -2, -3, -3, -1, -3,  -1, -1, -3, -3, -3,  -3, -1, -1, -1, -2,  -1, -2, -4,  // C
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:10:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, +6, -3, +6, +2,  -3, -1, -1, -3, -1,  -4, -3, +1, -1, +0,  -2, +0, -1, -3, -4,  -1, -3, +2,  // D
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:11:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, +2, -4, +2, +5,  -3, -2, +0, -3, +1,  -3, -2, +0, -1, +2,  +0, +0, -1, -2, -3,  -1, -2, +5,  // E
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:13:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, -3, -2, -3, -3,  +6, -3, -1, +0, -3,  +0, +0, -3, -4, -3,  -3, -2, -2, -1, +1,  -1, +3, -3,  // F
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:14:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +0, -1, -3, -1, -2,  -3, +6, -2, -4, -2,  -4, -3, +0, -2, -2,  -2, +0, -2, -3, -2,  -1, -3, -2,  // G
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:15:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, -1, -3, -1, +0,  -1, -2, +8, -3, -1,  -3, -2, +1, -2, +0,  +0, -1, -2, -3, -2,  -1, +2, +0,  // H
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:16:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -3, -1, -3, -3,  +0, -4, -3, +4, -3,  +2, +1, -3, -3, -3,  -3, -2, -1, +3, -3,  -1, -1, -3,  // I
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:17:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -1, -3, -1, +1,  -3, -2, -1, -3, +5,  -2, -1, +0, -1, +1,  +2, +0, -1, -2, -3,  -1, -2, +1,  // K
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -4, -1, -4, -3,  +0, -4, -3, +2, -2,  +4, +2, -3, -3, -2,  -2, -2, -1, +1, -2,  -1, -1, -3,  // L
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -3, -1, -3, -2,  +0, -3, -2, +1, -1,  +2, +5, -2, -2, +0,  -1, -1, -1, +1, -1,  -1, -1, -2,  // M
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, +1, -3, +1, +0,  -3, +0, +1, -3, +0,  -3, -2, +6, -2, +0,  +0, +1, +0, -3, -4,  -1, -2, +0,  // N
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -1, -3, -1, -1,  -4, -2, -2, -3, -1,  -3, -2, -2, +7, -1,  -2, -1, -1, -2, -4,  -1, -3, -1,  // P
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, +0, -3, +0, +2,  -3, -2, +0, -3, +1,  -2, +0, +0, -1, +5,  +1, +0, -1, -2, -2,  -1, -1, +2,  // Q
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -2, -3, -2, +0,  -3, -2, +0, -3, +2,  -2, -1, +0, -2, +1,  +5, -1, -1, -3, -3,  -1, -2, +0,  // R
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +1, +0, -1, +0, +0,  -2, +0, -1, -2, +0,  -2, -1, +1, -1, +0,  -1, +4, +1, -2, -3,  -1, -2, +0,  // S
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +0, -1, -1, -1, -1,  -2, -2, -2, -1, -1,  -1, -1, +0, -1, -1,  -1, +1, +5, +0, -2,  -1, -2, -1,  // T
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +0, -3, -1, -3, -2,  -1, -3, -3, +3, -2,  +1, +1, -3, -2, -2,  -3, -2, +0, +4, -3,  -1, -1, -2,  // V
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -3, -4, -2, -4, -3,  +1, -2, -2, -3, -3,  -2, -1, -4, -4, -2,  -3, -3, -2, -3,+11,  -1, +2, -3,  // W
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -1, -1, -1, -1,  -1, -1, -1, -1, -1,  -1, -1, -1, -1, -1,  -1, -1, -1, -1, -1,  -1, -1, -1,  // X
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, -3, -2, -3, -2,  +3, -3, +2, -1, -2,  -1, -1, -2, -3, -1,  -2, -2, -2, -1, +2,  -1, +7, -2,  // Y
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
color.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, +2, -4, +2, +5,  -3, -2, +0, -3, +1,  -3, -2, +0, -1, +2,  +0, +0, -1, -2, -3,  -1, -2, +5,  // Z
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                                                                             }
In file included from color.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function]
static int BlosumScore(char c1, char c2)
           ^
25 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cons.cpp -o cons.o
In file included from cons.cpp:7:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c diaglist.cpp -o diaglist.o
In file included from diaglist.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
        const unsigned uColCount = msa.GetColCount();
                       ^
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = msa.GetSeqCount();
                       ^
In file included from diffobjscore.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c diffpaths.cpp -o diffpaths.o
In file included from diffpaths.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c difftrees.cpp -o difftrees.o
difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
        const unsigned uLeafCount2 = Tree2.GetLeafCount();
                       ^
In file included from difftrees.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c difftreese.cpp -o difftreese.o
In file included from difftreese.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c distcalc.cpp -o distcalc.o
In file included from distcalc.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c distfunc.cpp -o distfunc.o
In file included from distfunc.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c distpwkimura.cpp -o distpwkimura.o
In file included from distpwkimura.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c domuscle.cpp -o domuscle.o
In file included from domuscle.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dosp.cpp -o dosp.o
In file included from dosp.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
                        const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
                                       ^
In file included from dpreglist.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c drawtree.cpp -o drawtree.o
In file included from drawtree.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c edgelist.cpp -o edgelist.o
In file included from edgelist.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c enumopts.cpp -o enumopts.o
In file included from enumopts.cpp:8:
./enums.h:12:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, Amino)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:47:1: note: expanded from here
"Amino"
^
In file included from enumopts.cpp:8:
./enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, DNA)
^˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:50:1: note: expanded from here
"DNA"
^
In file included from enumopts.cpp:8:
./enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, RNA)
^˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:53:1: note: expanded from here
"RNA"
^
In file included from enumopts.cpp:8:
./enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(ALPHA)
^˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:18:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, Protein)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Protein"
^
In file included from enumopts.cpp:8:
./enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, DNA)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"DNA"
^
In file included from enumopts.cpp:8:
./enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, RNA)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"RNA"
^
In file included from enumopts.cpp:8:
./enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, Auto)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Auto"
^
In file included from enumopts.cpp:8:
./enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(SEQTYPE)
^˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:25:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, Pseudo)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Pseudo"
^
In file included from enumopts.cpp:8:
./enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, MidLongestSpan)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"MidLongestSpan"
^
In file included from enumopts.cpp:8:
./enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, MinAvgLeafDist)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"MinAvgLeafDist"
^
In file included from enumopts.cpp:8:
./enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(ROOT)
^˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:31:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMA)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"UPGMA"
^
In file included from enumopts.cpp:8:
./enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMAMax)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"UPGMAMax"
^
In file included from enumopts.cpp:8:
./enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMAMin)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"UPGMAMin"
^
In file included from enumopts.cpp:8:
./enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMB)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"UPGMB"
^
In file included from enumopts.cpp:8:
./enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, NeighborJoining)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"NeighborJoining"
^
In file included from enumopts.cpp:8:
./enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(CLUSTER)
^˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:39:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(JOIN, NearestNeighbor)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"NearestNeighbor"
^
In file included from enumopts.cpp:8:
./enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(JOIN, NeighborJoining)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"NeighborJoining"
^
In file included from enumopts.cpp:8:
./enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(JOIN)
^˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:44:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Min)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Min"
^
In file included from enumopts.cpp:8:
./enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Avg)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Avg"
^
In file included from enumopts.cpp:8:
./enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Max)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Max"
^
In file included from enumopts.cpp:8:
./enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, NeighborJoining)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"NeighborJoining"
^
In file included from enumopts.cpp:8:
./enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Biased)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Biased"
^
In file included from enumopts.cpp:8:
./enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(LINKAGE)
^˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:52:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer6_6)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Kmer6_6"
^
In file included from enumopts.cpp:8:
./enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer20_3)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Kmer20_3"
^
In file included from enumopts.cpp:8:
./enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer20_4)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Kmer20_4"
^
In file included from enumopts.cpp:8:
./enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kbit20_3)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Kbit20_3"
^
In file included from enumopts.cpp:8:
./enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer4_6)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Kmer4_6"
^
In file included from enumopts.cpp:8:
./enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PctIdKimura)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"PctIdKimura"
^
In file included from enumopts.cpp:8:
./enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PctIdLog)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"PctIdLog"
^
In file included from enumopts.cpp:8:
./enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PWKimura)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"PWKimura"
^
In file included from enumopts.cpp:8:
./enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PWScoreDist)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"PWScoreDist"
^
In file included from enumopts.cpp:8:
./enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, ScoreDist)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"ScoreDist"
^
In file included from enumopts.cpp:8:
./enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Edit)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Edit"
^
In file included from enumopts.cpp:8:
./enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(DISTANCE)
^˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:66:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, LE)
^˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"LE"
^
In file included from enumopts.cpp:8:
./enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SP)
^˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"SP"
^
In file included from enumopts.cpp:8:
./enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SV)
^˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"SV"
^
In file included from enumopts.cpp:8:
./enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SPN)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"SPN"
^
In file included from enumopts.cpp:8:
./enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(PPSCORE)
^˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:73:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, None)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"None"
^
In file included from enumopts.cpp:8:
./enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, Henikoff)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Henikoff"
^
In file included from enumopts.cpp:8:
./enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, HenikoffPB)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"HenikoffPB"
^
In file included from enumopts.cpp:8:
./enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, GSC)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"GSC"
^
In file included from enumopts.cpp:8:
./enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, ClustalW)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"ClustalW"
^
In file included from enumopts.cpp:8:
./enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, ThreeWay)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"ThreeWay"
^
In file included from enumopts.cpp:8:
./enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(SEQWEIGHT)
^˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:82:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SP)                         // Sum of Pairs of sequences
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"SP"
^
In file included from enumopts.cpp:8:
./enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, DP)                         // Dynamic Programming score
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"DP"
^
In file included from enumopts.cpp:8:
./enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, XP)                         // Cross Pairs = sum of pairs between two MSAs
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"XP"
^
In file included from enumopts.cpp:8:
./enums.h:85:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, PS)                         // sum of Prof-Seq score for all seqs in MSA
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"PS"
^
In file included from enumopts.cpp:8:
./enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SPF)                        // sum of pairs, fast approximation
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"SPF"
^
In file included from enumopts.cpp:8:
./enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SPM)                        // sp if <= 100 seqs, spf otherwise
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"SPM"
^
In file included from enumopts.cpp:8:
./enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(OBJSCORE)
^˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:8:
./enums.h:91:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Full)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Full"
^
In file included from enumopts.cpp:8:
./enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Half)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Half"
^
In file included from enumopts.cpp:8:
./enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Ext)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^˜˜˜˜˜˜˜˜˜˜
<scratch space>:55:1: note: expanded from here
"Ext"
^
In file included from enumopts.cpp:8:
./enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(TERMGAPS)
^˜˜˜˜˜˜˜˜˜˜
{
enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^˜˜˜
In file included from enumopts.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
64 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c enumtostr.cpp -o enumtostr.o
In file included from enumtostr.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c estring.cpp -o estring.o
estring.cpp:397:8: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        if (nB > 0)
                            ^˜˜˜˜˜
estring.cpp:409:11: note: uninitialized use occurs here
                switch (cType)
                        ^˜˜˜˜
estring.cpp:397:4: note: remove the 'if' if its condition is always true
                        if (nB > 0)
                        ^˜˜˜˜˜˜˜˜˜˜
estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if (nA < 0)
                         ^˜˜˜˜˜
estring.cpp:409:11: note: uninitialized use occurs here
                switch (cType)
                        ^˜˜˜˜
estring.cpp:395:8: note: remove the 'if' if its condition is always true
                else if (nA < 0)
                     ^˜˜˜˜˜˜˜˜˜˜
estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (nB < 0)
                                 ^˜˜˜˜˜
estring.cpp:409:11: note: uninitialized use occurs here
                switch (cType)
                        ^˜˜˜˜
estring.cpp:386:9: note: remove the 'if' if its condition is always true
                        else if (nB < 0)
                             ^˜˜˜˜˜˜˜˜˜˜
estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning
                char cType;
                          ^
                           = '\0'
In file included from estring.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function]
static bool CanMultiplyEstrings(const short es1[], const short es2[])
            ^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fasta.cpp -o fasta.o
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
        unsigned uColCount = uInsane;
                 ^
fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
        unsigned uSeqCount = 0;
                 ^
In file included from fasta.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fasta2.cpp -o fasta2.o
In file included from fasta2.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastclust.cpp -o fastclust.o
In file included from fastclust.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastdist.cpp -o fastdist.o
In file included from fastdist.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastdistjones.cpp -o fastdistjones.o
In file included from fastdistjones.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastdistkbit.cpp -o fastdistkbit.o
In file included from fastdistkbit.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
                        double KD = KimuraDist(EstimatedPctId);
                               ^
In file included from fastdistkmer.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp:238:15: warning: unused variable 'pName1' [-Wunused-variable]
                const char *pName1 = s1.GetName();
                            ^
In file included from fastdistmafft.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function]
static void ListCount(const unsigned char Count[])
            ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
                const char *pName1 = s1.GetName();
                            ^
In file included from fastdistnuc.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable]
static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
                ^
fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function]
static void ListCount(const unsigned char Count[])
            ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastscorepath2.cpp -o fastscorepath2.o
In file included from fastscorepath2.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c finddiags.cpp -o finddiags.o
In file included from finddiags.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function]
static char *TupleToStr(int t)
             ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c finddiagsn.cpp -o finddiagsn.o
In file included from finddiagsn.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function]
static char *TupleToStr(int t)
             ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalign.cpp -o glbalign.o
In file included from glbalign.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalign352.cpp -o glbalign352.o
In file included from glbalign352.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbaligndiag.cpp -o glbaligndiag.o
In file included from glbaligndiag.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalignla.cpp -o glbalignla.o
In file included from glbalignla.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalignle.cpp -o glbalignle.o
In file included from glbalignle.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalignns.cpp -o glbalignns.o
In file included from glbalignns.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalignsimple.cpp -o glbalignsimple.o
In file included from glbalignsimple.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function]
static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
            ^
glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function]
static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
            ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalignsp.cpp -o glbalignsp.o
In file included from glbalignsp.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalignspn.cpp -o glbalignspn.o
In file included from glbalignspn.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
                const SCORE *ptrRowA = MxRowA[i];
                             ^
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
        const unsigned uPrefixCountA = uLengthA + 1;
                       ^
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
        const unsigned uPrefixCountB = uLengthB + 1;
                       ^
In file included from glbalignss.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function]
static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
             ^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch]
        switch (g_PPScore)
                ^
In file included from glbalndimer.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
                   ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c globals.cpp -o globals.o
In file included from globals.cpp:6:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c globalslinux.cpp -o globalslinux.o
In file included from globalslinux.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c globalsosx.cpp -o globalsosx.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c globalsother.cpp -o globalsother.o
In file included from globalsother.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c globalswin32.cpp -o globalswin32.o
In file included from globalswin32.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gonnet.cpp -o gonnet.o
In file included from gonnet.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable]
static SCORE Gonnet160[20][20] =
             ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gotowt.cpp -o gotowt.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c henikoffweight.cpp -o henikoffweight.o
In file included from henikoffweight.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c henikoffweightpb.cpp -o henikoffweightpb.o
In file included from henikoffweightpb.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c html.cpp -o html.o
In file included from html.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hydro.cpp -o hydro.o
In file included from hydro.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c intmath.cpp -o intmath.o
In file included from intmath.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c local.cpp -o local.o
In file included from local.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c main.cpp -o main.o
main.cpp:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   NULL
   ^˜˜˜
   {   }
/usr/local/clang4/bin/../lib/clang/4.0.0/include/stddef.h:100:18: note: expanded from macro 'NULL'
#    define NULL __null
                 ^˜˜˜˜˜
In file included from main.cpp:7:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
        const unsigned uSeqLength = s.Length();
                       ^
makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
                const PWPath &Path = Nodes[uNodeIndex].m_Path;
                              ^
makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
        const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
                       ^
In file included from makerootmsa.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function]
static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
            ^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c makerootmsab.cpp -o makerootmsab.o
In file included from makerootmsab.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c maketree.cpp -o maketree.o
In file included from maketree.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mhack.cpp -o mhack.o
In file included from mhack.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mpam200.cpp -o mpam200.o
In file included from mpam200.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c msa.cpp -o msa.o
In file included from msa.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function]
static void FmtChar(char c, unsigned uWidth)
            ^
msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function]
static void FmtInt(unsigned u, unsigned uWidth)
            ^
msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function]
static void FmtInt0(unsigned u, unsigned uWidth)
            ^
msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function]
static void FmtPad(unsigned n)
            ^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c msa2.cpp -o msa2.o
msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
        switch (Method)
                ^
msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
        const unsigned uColCountCat = uColCount1 + uColCount2;
                       ^
In file included from msa2.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c msadistkimura.cpp -o msadistkimura.o
In file included from msadistkimura.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c msf.cpp -o msf.o
In file included from msf.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function]
static const char *strfind(const char *s, const char *t)
                   ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c muscle.cpp -o muscle.o
In file included from muscle.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c muscleout.cpp -o muscleout.o
In file included from muscleout.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nucmx.cpp -o nucmx.o
In file included from nucmx.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nwdasimple.cpp -o nwdasimple.o
In file included from nwdasimple.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nwdasimple2.cpp -o nwdasimple2.o
In file included from nwdasimple2.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nwdasmall.cpp -o nwdasmall.o
In file included from nwdasmall.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nwrec.cpp -o nwrec.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nwsmall.cpp -o nwsmall.o
nwsmall.cpp:390:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
        default:
        ^˜˜˜˜˜˜
nwsmall.cpp:394:14: note: uninitialized use occurs here
        TB[i][j] |= Bit;
                    ^˜˜
nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning
        char Bit;
                ^
                 = '\0'
nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
        default:
        ^˜˜˜˜˜˜
nwsmall.cpp:412:14: note: uninitialized use occurs here
        TB[i][j] |= Bit;
                    ^˜˜
nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning
        char Bit;
                ^
                 = '\0'
nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
        default:
        ^˜˜˜˜˜˜
nwsmall.cpp:430:14: note: uninitialized use occurs here
        TB[i][j] |= Bit;
                    ^˜˜
nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning
        char Bit;
                ^
                 = '\0'
In file included from nwsmall.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function]
static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c)
                   ^
nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function]
static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c)
                   ^
6 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c objscore.cpp -o objscore.o
objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch]
        switch (OS)
                ^
In file included from objscore.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c objscore2.cpp -o objscore2.o
objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
        switch (g_TermGaps)
                ^
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
        bool bGapping1 = false;
             ^
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
        SCORE scoreGaps = 0;
              ^
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
        bool bGapping2 = false;
             ^
objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
        const unsigned uColCount2 = msa2.GetColCount();
                       ^
objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
                        const WEIGHT w = w1*w2;
                                     ^
In file included from objscore2.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
7 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c objscoreda.cpp -o objscoreda.o
In file included from objscoreda.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c onexception.cpp -o onexception.o
In file included from onexception.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c optionsR.cpp -o optionsR.o
optionsR.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "in",                           0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "in1",                          0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "in2",                          0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "out",                          0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxIters",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxHours",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapOpen",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapOpen2",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapExtend",            0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapExtend2",           0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapAmbig",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Center",                       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SmoothScoreCeil",      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MinBestColScore",      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MinSmoothScore",       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ObjScore",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SmoothWindow",         0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "RefineWindow",         0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "FromWindow",           0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ToWindow",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SaveWindow",           0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "WindowOffset",         0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "FirstWindow",          0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "AnchorSpacing",        0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Log",                          0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "LogA",                         0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxTrees",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SUEFF",                        0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Distance",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Distance1",            0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Distance2",            0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Weight",                       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Weight1",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Weight2",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Cluster",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Cluster1",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Cluster2",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Root1",                        0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Root2",                        0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Tree1",                        0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Tree2",                        0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "UseTree",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "UseTree_NoWarn",       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DiagLength",           0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DiagMargin",           0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DiagBreak",            0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Hydro",                        0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "HydroFactor",          0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SPScore",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SeqType",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxMB",                        0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ComputeWeights",       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxSubFam",            0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ScoreFile",            0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "TermGaps",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "FASTAOut",                     0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "CLWOut",                       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "CLWStrictOut",         0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                        }
optionsR.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "HTMLOut",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MSFOut",                       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:81:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PHYIOut",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:82:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PHYSOut",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:83:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Matrix",                       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:84:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DistMx1",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:85:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DistMx2",                      0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:86:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Weight",                       0,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                }
optionsR.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "LE",                                   false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SP",                                   false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SV",                                   false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SPN",                                  false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Core",                                 false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "NoCore",                               false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Diags1",                               false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Diags2",                               false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Diags",                                false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Quiet",                                false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MSF",                                  false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Verbose",                              false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Anchors",                              false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "NoAnchors",                    false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                    }
optionsR.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Refine",                               false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "RefineW",                              false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SW",                                   false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Profile",                              false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PPScore",                              false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ClusterOnly",                  false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                    }
optionsR.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Brenner",                              false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Dimer",                                false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "clw",                                  false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "clwstrict",                    false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                    }
optionsR.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "HTML",                                 false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Version",                              false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Stable",                               false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Group",                                false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "FASTA",                                false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ProfDB",                               false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PAS",                                  false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PHYI",                                 false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:124:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PHYS",                                 false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:125:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "TomHydro",                             false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
optionsR.cpp:126:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MakeTree",                             false,
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
        {                                            }
In file included from optionsR.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
102 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c outweights.cpp -o outweights.o
In file included from outweights.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:9:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   408,    20,    54,    52,  -182,   179,   -68,   109,   -35,   -47,    39,   106,   206,   -14,   -12,   257,   293,   191,  -306,  -219,     0,     0,     0, // A
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:10:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
    20,  1190,  -228,  -295,    94,     6,    63,  -131,  -184,  -176,  -112,   -29,  -122,  -195,    49,   185,    13,   -49,   199,   333,     0,     0,     0, // C
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
    {                                                                                                                                                           }
pam200mafft.cpp:11:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
    54,  -228,   645,   516,  -399,   168,    98,  -225,    75,  -341,  -235,   352,  -149,   142,   -44,    65,     7,  -147,  -418,  -128,     0,     0,     0, // D
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
    {                                                                                                                                                           }
pam200mafft.cpp:12:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
    52,  -295,   516,   630,  -460,   145,    45,  -225,   195,  -307,  -222,   186,  -121,   299,    54,   -10,   -36,  -130,  -366,  -285,     0,     0,     0, // E
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
    {                                                                                                                                                           }
pam200mafft.cpp:13:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  -182,    94,  -399,  -460,   908,  -387,    82,   100,  -423,   340,    87,  -216,  -160,  -274,  -307,   -31,  -153,    51,    19,   604,     0,     0,     0, // F
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
  {                                                                                                                                                             }
pam200mafft.cpp:14:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   179,     6,   168,   145,  -387,   682,   -94,  -196,   -14,  -304,  -226,    99,   -57,   -48,   117,   175,    41,   -73,   -38,  -329,     0,     0,     0, // G
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:15:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -68,    63,    98,    45,    82,   -94,   786,  -185,   164,   -72,  -132,   258,    86,   388,   277,    55,   -15,  -197,  -181,   488,     0,     0,     0, // H
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:16:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   109,  -131,  -225,  -225,   100,  -196,  -185,   574,  -204,   308,   411,   -94,   -95,  -202,  -188,     1,   182,   489,  -254,  -133,     0,     0,     0, // I
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:17:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -35,  -184,    75,   195,  -423,   -14,   164,  -204,   652,  -229,   -98,   206,   -66,   335,   486,    22,    39,  -207,  -196,  -244,     0,     0,     0, // K
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:18:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -47,  -176,  -341,  -307,   340,  -304,   -72,   308,  -229,   611,   389,  -203,    73,   -66,  -150,   -49,   -21,   259,   -46,    -9,     0,     0,     0, // L
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:19:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
    39,  -112,  -235,  -222,    87,  -226,  -132,   411,   -98,   389,   776,  -111,   -78,  -104,  -109,   -29,   149,   351,  -209,  -162,     0,     0,     0, // M
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
    {                                                                                                                                                           }
pam200mafft.cpp:20:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   106,   -29,   352,   186,  -216,    99,   258,   -94,   206,  -203,  -111,   536,    -1,   108,    93,   260,   188,   -98,  -359,    12,     0,     0,     0, // N
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:21:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   206,  -122,  -149,  -121,  -160,   -57,    86,   -95,   -66,    73,   -78,    -1,   756,   142,    25,   241,   159,   -55,  -353,  -206,     0,     0,     0, // P
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:22:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -14,  -195,   142,   299,  -274,   -48,   388,  -202,   335,   -66,  -104,   108,   142,   655,   321,     7,   -15,  -175,  -223,   -53,     0,     0,     0, // Q
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:23:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -12,    49,   -44,    54,  -307,   117,   277,  -188,   486,  -150,  -109,    93,    25,   321,   626,    48,    16,  -181,   124,  -113,     0,     0,     0, // R
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:24:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   257,   185,    65,   -10,   -31,   175,    55,     1,    22,   -49,   -29,   260,   241,     7,    48,   373,   279,    28,  -193,   -35,     0,     0,     0, // S
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:25:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   293,    13,     7,   -36,  -153,    41,   -15,   182,    39,   -21,   149,   188,   159,   -15,    16,   279,   442,   163,  -323,  -170,     0,     0,     0, // T
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:26:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   191,   -49,  -147,  -130,    51,   -73,  -197,   489,  -207,   259,   351,   -98,   -55,  -175,  -181,    28,   163,   525,  -225,  -177,     0,     0,     0, // V
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
   {                                                                                                                                                            }
pam200mafft.cpp:27:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  -306,   199,  -418,  -366,    19,   -38,  -181,  -254,  -196,   -46,  -209,  -359,  -353,  -223,   124,  -193,  -323,  -225,  1495,    83,     0,     0,     0, // W
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
  {                                                                                                                                                             }
pam200mafft.cpp:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  -219,   333,  -128,  -285,   604,  -329,   488,  -133,  -244,    -9,  -162,    12,  -206,   -53,  -113,   -35,  -170,  -177,    83,   999,     0,     0,     0, // Y
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
  {                                                                                                                                                             }
pam200mafft.cpp:29:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // B
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
     {                                                                                                                                                          }
pam200mafft.cpp:30:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // Z
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
     {                                                                                                                                                          }
pam200mafft.cpp:31:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // X
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
     {                                                                                                                                                          }
In file included from pam200mafft.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable]
static float PAM200[23][23] =
             ^
25 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c params.cpp -o params.o
params.cpp:445:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
        switch (g_PPScore)
                ^
params.cpp:659:2: warning: expression result unused [-Wunused-value]
        g_ptrScoreMatrix;
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
params.cpp:655:14: warning: unused variable 'VTML_SP' [-Wunused-variable]
        SCOREMATRIX VTML_SP;
                    ^
params.cpp:654:14: warning: unused variable 'PAM200NoCenter' [-Wunused-variable]
        SCOREMATRIX PAM200NoCenter;
                    ^
params.cpp:657:14: warning: unused variable 'NUC_SP' [-Wunused-variable]
        SCOREMATRIX NUC_SP;
                    ^
params.cpp:653:14: warning: unused variable 'PAM200' [-Wunused-variable]
        SCOREMATRIX PAM200;
                    ^
params.cpp:652:14: warning: unused variable 'VTML_LA' [-Wunused-variable]
        SCOREMATRIX VTML_LA;
                    ^
params.cpp:656:14: warning: unused variable 'VTML_SPNoCenter' [-Wunused-variable]
        SCOREMATRIX VTML_SPNoCenter;
                    ^
In file included from params.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
9 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c phy.cpp -o phy.o
phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
        double dEdgeLength = GetEdgeLength(uNode1, uNode2);
               ^
In file included from phy.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c phy2.cpp -o phy2.o
In file included from phy2.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c phy3.cpp -o phy3.o
phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
        const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
                     ^
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
        unsigned uMaxTo = NULL_NEIGHBOR;
                 ^
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
        double dAllMaxDist = -1e20;
               ^
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
        const unsigned uLeafCount = tree.GetLeafCount();
                       ^
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
        unsigned uMaxFrom = NULL_NEIGHBOR;
                 ^
In file included from phy3.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function]
static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
            ^
7 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c phy4.cpp -o phy4.o
In file included from phy4.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c phyfromclust.cpp -o phyfromclust.o
In file included from phyfromclust.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c phyfromfile.cpp -o phyfromfile.o
In file included from phyfromfile.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c physeq.cpp -o physeq.o
In file included from physeq.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c phytofile.cpp -o phytofile.o
In file included from phytofile.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c posgap.cpp -o posgap.o
In file included from posgap.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ppscore.cpp -o ppscore.o
In file included from ppscore.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c profdb.cpp -o profdb.o
In file included from profdb.cpp:9:
In file included from ./clustsetmsa.h:8:
./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
                switch(m_Distance)
                       ^
In file included from profdb.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c profile.cpp -o profile.o
In file included from profile.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
        switch (g_Alpha)
                ^
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
        unsigned uHydrophobicRunLength = 0;
                 ^
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = a.GetSeqCount();
                       ^
In file included from profilefrommsa.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
                   ^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c progalign.cpp -o progalign.o
progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
        const unsigned uIterCount = uSeqCount - 1;
                       ^
In file included from progalign.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c progress.cpp -o progress.o
In file included from progress.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c progressivealign.cpp -o progressivealign.o
In file included from progressivealign.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pwpath.cpp -o pwpath.o
pwpath.cpp:79:16: warning: unused variable 'LastEdge' [-Wunused-variable]
        const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
                      ^
pwpath.cpp:212:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
        unsigned uEdgeIndex = 0;
                 ^
In file included from pwpath.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c readmx.cpp -o readmx.o
In file included from readmx.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function]
static unsigned MxCharToLetter(char c)
                ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c realigndiffs.cpp -o realigndiffs.o
In file included from realigndiffs.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c realigndiffse.cpp -o realigndiffse.o
realigndiffse.cpp:72:13: warning: unused variable 'uNewRight' [-Wunused-variable]
                        unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
                                 ^
realigndiffse.cpp:75:13: warning: unused variable 'uOldRight' [-Wunused-variable]
                        unsigned uOldRight = OldTree.GetRight(uOld);
                                 ^
In file included from realigndiffse.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c redblack.cpp -o redblack.o
In file included from redblack.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c refine.cpp -o refine.o
In file included from refine.cpp:9:
In file included from ./clustsetmsa.h:8:
./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
                switch(m_Distance)
                       ^
In file included from refine.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c refinehoriz.cpp -o refinehoriz.o
refinehoriz.cpp:256:4: warning: variable 'bRight' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                        default:
                        ^˜˜˜˜˜˜
refinehoriz.cpp:259:56: note: uninitialized use occurs here
                        RefineHeightParts(msaIn, tree, Internals, bReverse, bRight,
                                                                            ^˜˜˜˜˜
refinehoriz.cpp:247:15: note: initialize the variable 'bRight' to silence this warning
                        bool bRight;
                                   ^
                                    = false
In file included from refinehoriz.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
        const unsigned uNodeCount = tree.GetNodeCount();
                       ^
In file included from refinesubfams.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c refinetree.cpp -o refinetree.o
In file included from refinetree.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c refinetreee.cpp -o refinetreee.o
In file included from refinetreee.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c refinevert.cpp -o refinevert.o
In file included from refinevert.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c refinew.cpp -o refinew.o
refinew.cpp:26:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
        const unsigned uColCountCat = uColCount1 + uColCount2;
                       ^
refinew.cpp:129:13: warning: unused variable 'uOutCols' [-Wunused-variable]
                        unsigned uOutCols = msaOut.GetColCount();
                                 ^
In file included from refinew.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c savebest.cpp -o savebest.o
In file included from savebest.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c scoredist.cpp -o scoredist.o
In file included from scoredist.cpp:3:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable]
static const double Dayhoff_CalibrationFactor = 1.3370;
                    ^
scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable]
static const double MV_CalibrationFactor = 1.1775;
                    ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c scoregaps.cpp -o scoregaps.o
In file included from scoregaps.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function]
static void FreeGapInfo(GAPINFO *GI)
            ^
scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function]
static SCORE Penalty(unsigned Length, bool Term)
             ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c scorehistory.cpp -o scorehistory.o
In file included from scorehistory.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c scorepp.cpp -o scorepp.o
In file included from scorepp.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c seq.cpp -o seq.o
In file included from seq.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c seqvect.cpp -o seqvect.o
seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference]
        return (Seq &) *((Seq *) 0);
                       ^˜˜˜˜˜˜˜˜˜˜˜
In file included from seqvect.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable]
const size_t MAX_FASTA_LINE = 16000;
             ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c setblosumweights.cpp -o setblosumweights.o
In file included from setblosumweights.cpp:42:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c setgscweights.cpp -o setgscweights.o
In file included from setgscweights.cpp:104:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c setnewhandler.cpp -o setnewhandler.o
In file included from setnewhandler.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c spfast.cpp -o spfast.o
spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = msa.GetSeqCount();
                       ^
In file included from spfast.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function]
static const char *GapTypeToStr(int GapType)
                   ^
spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function]
static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
             ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sptest.cpp -o sptest.o
In file included from sptest.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c stabilize.cpp -o stabilize.o
In file included from stabilize.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c subfam.cpp -o subfam.o
subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
        int NotUsed = system(CmdLine);
            ^
In file included from subfam.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c subfams.cpp -o subfams.o
subfams.cpp:44:25: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        for (unsigned i = 0; i < uNodeCount; ++i)
                             ˜ ^ ˜˜˜˜˜˜˜˜˜˜
In file included from subfams.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
subfams.cpp:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function]
static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
            ^
subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function]
static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
            ^
subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function]
static void Relax(DistFunc &DF, unsigned u, unsigned v)
            ^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sw.cpp -o sw.o
In file included from sw.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function]
static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
            ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c termgaps.cpp -o termgaps.o
In file included from termgaps.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c textfile.cpp -o textfile.o
textfile.cpp:104:6: warning: unused variable 'i' [-Wunused-variable]
        int i = fputc(c, m_ptrFile);
            ^
textfile.cpp:117:6: warning: unused variable 'iError' [-Wunused-variable]
        int iError = fputs(szLine, m_ptrFile);
            ^
In file included from textfile.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c threewaywt.cpp -o threewaywt.o
In file included from threewaywt.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tomhydro.cpp -o tomhydro.o
In file included from tomhydro.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c traceback.cpp -o traceback.o
traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
        const unsigned uPrefixCountB = uLengthB + 1;
                       ^
traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                default:
                ^˜˜˜˜˜˜
traceback.cpp:202:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSI))
                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:202:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:186:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSI))
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSD))
                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:202:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:150:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSD))
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(scoreSM, Score))
                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:202:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:112:9: note: remove the 'if' if its condition is always true
                        else if (EQ(scoreSM, Score))
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
                char cPrevEdgeType;
                                  ^
                                   = '\0'
In file included from traceback.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
6 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracebackopt.cpp -o tracebackopt.o
In file included from tracebackopt.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracebacksw.cpp -o tracebacksw.o
tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
        const unsigned uPrefixCountB = uLengthB + 1;
                       ^
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
        SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
              ^
tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                default:
                ^˜˜˜˜˜˜
tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSI))
                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSI))
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSD))
                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSD))
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(scoreMatch, Score))
                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true
                        else if (EQ(scoreMatch, Score))
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
                char cPrevEdgeType;
                                  ^
                                   = '\0'
In file included from tracebacksw.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
7 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c treefrommsa.cpp -o treefrommsa.o
In file included from treefrommsa.cpp:5:
In file included from ./clustsetmsa.h:8:
./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
                switch(m_Distance)
                       ^
In file included from treefrommsa.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c typetostr.cpp -o typetostr.o
In file included from typetostr.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c upgma2.cpp -o upgma2.o
upgma2.cpp:272:4: warning: variable 'dtNewDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                        default:
                        ^˜˜˜˜˜˜
upgma2.cpp:292:17: note: uninitialized use occurs here
                        g_Dist[vL] = dtNewDist;
                                     ^˜˜˜˜˜˜˜˜
upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning
                        dist_t dtNewDist;
                                        ^
                                         = 0.0
upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        0,  2, 14, 14, 20,
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
                        {                }
upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        2,  0, 14, 14, 20,
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
                        {                }
upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        14, 14,  0,  4, 20,
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
                        {                 }
upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        14, 14,  4,  0, 20,
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
                        {                 }
upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        20, 20, 20, 20,  0,
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
                        {                 }
In file included from upgma2.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function]
static void ListState()
            ^
8 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c usage.cpp -o usage.o
In file included from usage.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c validateids.cpp -o validateids.o
In file included from validateids.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vtml2.cpp -o vtml2.o
In file included from vtml2.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c writescorefile.cpp -o writescorefile.o
writescorefile.cpp:37:4: warning: variable 'Score' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                        default:
                        ^˜˜˜˜˜˜
writescorefile.cpp:40:12: note: uninitialized use occurs here
                        dSum += Score;
                                ^˜˜˜˜
writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning
                        double Score;
                                    ^
                                     = 0.0
In file included from writescorefile.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o muscle.so aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignla.o glbalignle.o glbalignns.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o gotowt.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o optionsR.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o redblack.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/muscle.Rcheck/muscle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (muscle)

Tests output


Example timings

muscle.Rcheck/muscle-Ex.timings

nameusersystemelapsed
muscle-package0.0010.0000.001
muscle2.4400.0432.538