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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL muscle
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘muscle’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c alpha.cpp -o alpha.o
alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
switch (Alpha)
^~~~~
alpha.cpp:84:10: note: add missing switch cases
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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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:167:10: note: add missing switch cases
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:295:10: note: add missing switch cases
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)
^~~~~~~~~~~
clust.cpp:611:10: note: add missing switch cases
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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cluster.cpp -o cluster.o
cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
bool bFound = false;
^
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
double dMaxDist = 0.0;
^
In file included from 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)
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
const unsigned uSeqCount = msa.GetSeqCount();
^
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
const unsigned uColCount = msa.GetColCount();
^
In file included from 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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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>:112:1: 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>:115:1: 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>:118:1: 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>:122:1: 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>:125:1: 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>:128:1: 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>:131:1: 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>:135:1: 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>:138:1: 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>:141:1: 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>:145:1: 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>:148:1: 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>:151:1: 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>:154:1: 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>:157:1: 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>:161:1: 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>:164:1: 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>:168:1: 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>:171:1: 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>:174:1: 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>:177:1: 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>:180:1: 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>:184:1: 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>:187:1: 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>:190:1: 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>:193:1: 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>:196:1: 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>:199:1: 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>:202:1: 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>:205:1: 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>:208:1: 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>:211:1: 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>:214:1: 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>:218:1: 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>:221:1: 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>:224:1: 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>:227:1: 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>:231:1: 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>:234:1: 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>:237:1: 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>:240:1: 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>:243:1: 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>:246:1: 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>:250:1: 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>:253:1: 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>:256:1: 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>:259:1: 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>:262:1: 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>:265:1: 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>:269:1: 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>:272:1: 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>:275:1: 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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fasta.cpp -o fasta.o
fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
unsigned uSeqCount = 0;
^
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
unsigned uColCount = uInsane;
^
In file included from 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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
const SCORE *ptrRowA = MxRowA[i];
^
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
const unsigned uPrefixCountB = uLengthB + 1;
^
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
const unsigned uPrefixCountA = uLengthA + 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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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)
^~~~~~~~~
glbalndimer.cpp:123:10: note: add missing switch cases
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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c globals.cpp -o globals.o
globals.cpp:107:2: error: use of undeclared identifier 'error'
error("error in muscle\n");
^
1 error generated.
make: *** [globals.o] Error 1
ERROR: compilation failed for package ‘muscle’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/muscle’
