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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/4.6/Resources/library’
* installing *source* package ‘muscle’ ...
** this is package ‘muscle’ version ‘3.53.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligngivenpath.cpp -o aligngivenpath.o
aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
186 | const unsigned uLengthA = msaA.GetColCount();
| ^~~~~~~~
aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
187 | const unsigned uLengthB = msaB.GetColCount();
| ^~~~~~~~
aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
335 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
336 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
346 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
354 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
aligngivenpath.cpp:654:11: warning: variable 'uColIndexA' set but not used [-Wunused-but-set-variable]
654 | unsigned uColIndexA = 0;
| ^
aligngivenpath.cpp:655:11: warning: variable 'uColIndexB' set but not used [-Wunused-but-set-variable]
655 | unsigned uColIndexB = 0;
| ^
In file included from aligngivenpath.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligngivenpathsw.cpp -o aligngivenpathsw.o
aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
58 | const unsigned uLengthA = msaA.GetColCount();
| ^~~~~~~~
aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
59 | const unsigned uLengthB = msaB.GetColCount();
| ^~~~~~~~
aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
204 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
205 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
215 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
223 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
7 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alpha.cpp -o alpha.o
alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
84 | switch (Alpha)
| ^~~~~
alpha.cpp:84:10: note: add missing switch cases
84 | switch (Alpha)
| ^
85 | {
86 | case ALPHA_Amino:
87 | return 20;
88 |
89 | case ALPHA_RNA:
90 | case ALPHA_DNA:
91 | return 4;
92 | }
In file included from alpha.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c anchors.cpp -o anchors.o
anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
162 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function]
53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
| ^~~~~~~~~~~~~~~~~
anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function]
105 | static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
| ^~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
146 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function]
15 | static const char *BitsToStr(char Bits)
| ^~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable]
7 | static float Blosum62LA[20][20] =
| ^~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clust.cpp -o clust.o
clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
167 | switch (m_JoinStyle)
| ^~~~~~~~~~~
clust.cpp:167:10: note: add missing switch cases
167 | switch (m_JoinStyle)
| ^
168 | {
169 | case JOIN_NearestNeighbor:
clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
184 | const unsigned uClusterCount = GetClusterCount();
| ^~~~~~~~~~~~~
clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
204 | const unsigned uClusterCount = GetClusterCount();
| ^~~~~~~~~~~~~
clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
295 | switch (m_CentroidStyle)
| ^~~~~~~~~~~~~~~
clust.cpp:295:10: note: add missing switch cases
295 | switch (m_CentroidStyle)
| ^
clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
360 | const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
| ^~~~~~~
clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
611 | switch (m_JoinStyle)
| ^~~~~~~~~~~
clust.cpp:611:10: note: add missing switch cases
611 | switch (m_JoinStyle)
| ^
612 | {
613 | case JOIN_NearestNeighbor:
In file included from clust.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
7 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cluster.cpp -o cluster.o
cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
284 | bool bFound = false;
| ^
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
267 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function]
10 | static inline float Max(float d1, float d2)
| ^~~
cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function]
15 | static inline float Mean(float d1, float d2)
| ^~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c color.cpp -o color.o
color.cpp:7:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
7 | +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]
8 | -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]
9 | +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]
10 | -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]
11 | -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]
13 | -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]
14 | +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]
15 | -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]
16 | -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]
17 | -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]
19 | -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]
20 | -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]
21 | -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]
22 | -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]
23 | -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]
25 | -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]
26 | +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]
27 | +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]
28 | +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]
29 | -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]
31 | -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]
32 | -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]
33 | -1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // Z
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
color.cpp:126:11: warning: variable 'uCharCount' set but not used [-Wunused-but-set-variable]
126 | unsigned uCharCount = 0;
| ^
In file included from color.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function]
72 | static int BlosumScore(char c1, char c2)
| ^~~~~~~~~~~
26 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
76 | const unsigned uSeqCount = msa.GetSeqCount();
| ^~~~~~~~~
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
77 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c difftrees.cpp -o difftrees.o
difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
161 | const unsigned uLeafCount2 = Tree2.GetLeafCount();
| ^~~~~~~~~~~
difftrees.cpp:296:11: warning: variable 'uDiffCount' set but not used [-Wunused-but-set-variable]
296 | unsigned uDiffCount = 0;
| ^
In file included from difftrees.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c domuscle.cpp -o domuscle.o
domuscle.cpp:71:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
71 | sprintf(NewFileName, "%s/%s", Path, FileName);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from domuscle.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
82 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
12 | c(ALPHA, Amino)
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:17:1: note: expanded from here
17 | "Amino"
| ^
In file included from enumopts.cpp:8:
./enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
13 | c(ALPHA, DNA)
| ^~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:20:1: note: expanded from here
20 | "DNA"
| ^
In file included from enumopts.cpp:8:
./enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
14 | c(ALPHA, RNA)
| ^~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:23:1: note: expanded from here
23 | "RNA"
| ^
In file included from enumopts.cpp:8:
./enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
15 | e(ALPHA)
| ^~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
18 | c(SEQTYPE, Protein)
| ^~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:27:1: note: expanded from here
27 | "Protein"
| ^
In file included from enumopts.cpp:8:
./enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
19 | c(SEQTYPE, DNA)
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:30:1: note: expanded from here
30 | "DNA"
| ^
In file included from enumopts.cpp:8:
./enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
20 | c(SEQTYPE, RNA)
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:33:1: note: expanded from here
33 | "RNA"
| ^
In file included from enumopts.cpp:8:
./enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
21 | c(SEQTYPE, Auto)
| ^~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:36:1: note: expanded from here
36 | "Auto"
| ^
In file included from enumopts.cpp:8:
./enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
22 | e(SEQTYPE)
| ^~~~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
25 | c(ROOT, Pseudo)
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:40:1: note: expanded from here
40 | "Pseudo"
| ^
In file included from enumopts.cpp:8:
./enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
26 | c(ROOT, MidLongestSpan)
| ^~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:43:1: note: expanded from here
43 | "MidLongestSpan"
| ^
In file included from enumopts.cpp:8:
./enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
27 | c(ROOT, MinAvgLeafDist)
| ^~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:46:1: note: expanded from here
46 | "MinAvgLeafDist"
| ^
In file included from enumopts.cpp:8:
./enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
28 | e(ROOT)
| ^~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
31 | c(CLUSTER, UPGMA)
| ^~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:50:1: note: expanded from here
50 | "UPGMA"
| ^
In file included from enumopts.cpp:8:
./enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
32 | c(CLUSTER, UPGMAMax)
| ^~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:53:1: note: expanded from here
53 | "UPGMAMax"
| ^
In file included from enumopts.cpp:8:
./enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
33 | c(CLUSTER, UPGMAMin)
| ^~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:56:1: note: expanded from here
56 | "UPGMAMin"
| ^
In file included from enumopts.cpp:8:
./enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
34 | c(CLUSTER, UPGMB)
| ^~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:59:1: note: expanded from here
59 | "UPGMB"
| ^
In file included from enumopts.cpp:8:
./enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
35 | c(CLUSTER, NeighborJoining)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:62:1: note: expanded from here
62 | "NeighborJoining"
| ^
In file included from enumopts.cpp:8:
./enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
36 | e(CLUSTER)
| ^~~~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
39 | c(JOIN, NearestNeighbor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:66:1: note: expanded from here
66 | "NearestNeighbor"
| ^
In file included from enumopts.cpp:8:
./enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
40 | c(JOIN, NeighborJoining)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:69:1: note: expanded from here
69 | "NeighborJoining"
| ^
In file included from enumopts.cpp:8:
./enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
41 | e(JOIN)
| ^~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
44 | c(LINKAGE, Min)
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:73:1: note: expanded from here
73 | "Min"
| ^
In file included from enumopts.cpp:8:
./enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
45 | c(LINKAGE, Avg)
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:76:1: note: expanded from here
76 | "Avg"
| ^
In file included from enumopts.cpp:8:
./enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
46 | c(LINKAGE, Max)
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:79:1: note: expanded from here
79 | "Max"
| ^
In file included from enumopts.cpp:8:
./enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
47 | c(LINKAGE, NeighborJoining)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:82:1: note: expanded from here
82 | "NeighborJoining"
| ^
In file included from enumopts.cpp:8:
./enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
48 | c(LINKAGE, Biased)
| ^~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:85:1: note: expanded from here
85 | "Biased"
| ^
In file included from enumopts.cpp:8:
./enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
49 | e(LINKAGE)
| ^~~~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
52 | c(DISTANCE, Kmer6_6)
| ^~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:89:1: note: expanded from here
89 | "Kmer6_6"
| ^
In file included from enumopts.cpp:8:
./enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
53 | c(DISTANCE, Kmer20_3)
| ^~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:92:1: note: expanded from here
92 | "Kmer20_3"
| ^
In file included from enumopts.cpp:8:
./enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
54 | c(DISTANCE, Kmer20_4)
| ^~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:95:1: note: expanded from here
95 | "Kmer20_4"
| ^
In file included from enumopts.cpp:8:
./enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
55 | c(DISTANCE, Kbit20_3)
| ^~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:98:1: note: expanded from here
98 | "Kbit20_3"
| ^
In file included from enumopts.cpp:8:
./enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
56 | c(DISTANCE, Kmer4_6)
| ^~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:101:1: note: expanded from here
101 | "Kmer4_6"
| ^
In file included from enumopts.cpp:8:
./enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
57 | c(DISTANCE, PctIdKimura)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:104:1: note: expanded from here
104 | "PctIdKimura"
| ^
In file included from enumopts.cpp:8:
./enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
58 | c(DISTANCE, PctIdLog)
| ^~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:107:1: note: expanded from here
107 | "PctIdLog"
| ^
In file included from enumopts.cpp:8:
./enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
59 | c(DISTANCE, PWKimura)
| ^~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:110:1: note: expanded from here
110 | "PWKimura"
| ^
In file included from enumopts.cpp:8:
./enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
60 | c(DISTANCE, PWScoreDist)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:113:1: note: expanded from here
113 | "PWScoreDist"
| ^
In file included from enumopts.cpp:8:
./enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
61 | c(DISTANCE, ScoreDist)
| ^~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:116:1: note: expanded from here
116 | "ScoreDist"
| ^
In file included from enumopts.cpp:8:
./enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
62 | c(DISTANCE, Edit)
| ^~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:119:1: note: expanded from here
119 | "Edit"
| ^
In file included from enumopts.cpp:8:
./enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
63 | e(DISTANCE)
| ^~~~~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
66 | c(PPSCORE, LE)
| ^~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:123:1: note: expanded from here
123 | "LE"
| ^
In file included from enumopts.cpp:8:
./enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
67 | c(PPSCORE, SP)
| ^~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:126:1: note: expanded from here
126 | "SP"
| ^
In file included from enumopts.cpp:8:
./enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
68 | c(PPSCORE, SV)
| ^~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:129:1: note: expanded from here
129 | "SV"
| ^
In file included from enumopts.cpp:8:
./enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
69 | c(PPSCORE, SPN)
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:132:1: note: expanded from here
132 | "SPN"
| ^
In file included from enumopts.cpp:8:
./enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
70 | e(PPSCORE)
| ^~~~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
73 | c(SEQWEIGHT, None)
| ^~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:136:1: note: expanded from here
136 | "None"
| ^
In file included from enumopts.cpp:8:
./enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
74 | c(SEQWEIGHT, Henikoff)
| ^~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:139:1: note: expanded from here
139 | "Henikoff"
| ^
In file included from enumopts.cpp:8:
./enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
75 | c(SEQWEIGHT, HenikoffPB)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:142:1: note: expanded from here
142 | "HenikoffPB"
| ^
In file included from enumopts.cpp:8:
./enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
76 | c(SEQWEIGHT, GSC)
| ^~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:145:1: note: expanded from here
145 | "GSC"
| ^
In file included from enumopts.cpp:8:
./enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
77 | c(SEQWEIGHT, ClustalW)
| ^~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:148:1: note: expanded from here
148 | "ClustalW"
| ^
In file included from enumopts.cpp:8:
./enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
78 | c(SEQWEIGHT, ThreeWay)
| ^~~~~~~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:151:1: note: expanded from here
151 | "ThreeWay"
| ^
In file included from enumopts.cpp:8:
./enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
79 | e(SEQWEIGHT)
| ^~~~~~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
82 | c(OBJSCORE, SP) // Sum of Pairs of sequences
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:155:1: note: expanded from here
155 | "SP"
| ^
In file included from enumopts.cpp:8:
./enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
83 | c(OBJSCORE, DP) // Dynamic Programming score
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:158:1: note: expanded from here
158 | "DP"
| ^
In file included from enumopts.cpp:8:
./enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
84 | c(OBJSCORE, XP) // Cross Pairs = sum of pairs between two MSAs
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:161:1: note: expanded from here
161 | "XP"
| ^
In file included from enumopts.cpp:8:
./enums.h:85:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
85 | c(OBJSCORE, PS) // sum of Prof-Seq score for all seqs in MSA
| ^~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:164:1: note: expanded from here
164 | "PS"
| ^
In file included from enumopts.cpp:8:
./enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
86 | c(OBJSCORE, SPF) // sum of pairs, fast approximation
| ^~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:167:1: note: expanded from here
167 | "SPF"
| ^
In file included from enumopts.cpp:8:
./enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
87 | c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise
| ^~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:170:1: note: expanded from here
170 | "SPM"
| ^
In file included from enumopts.cpp:8:
./enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
88 | e(OBJSCORE)
| ^~~~~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
91 | c(TERMGAPS, Full)
| ^~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:174:1: note: expanded from here
174 | "Full"
| ^
In file included from enumopts.cpp:8:
./enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
92 | c(TERMGAPS, Half)
| ^~~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:177:1: note: expanded from here
177 | "Half"
| ^
In file included from enumopts.cpp:8:
./enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
93 | c(TERMGAPS, Ext)
| ^~~~~~~~~~~~~~~~
| {
enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:180:1: note: expanded from here
180 | "Ext"
| ^
In file included from enumopts.cpp:8:
./enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
94 | e(TERMGAPS)
| ^~~~~~~~~~~
| {
enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
64 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c enumtostr.cpp -o enumtostr.o
In file included from enumtostr.cpp:10:
./enums.h:15:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
15 | e(ALPHA)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:22:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
22 | e(SEQTYPE)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:28:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
28 | e(ROOT)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:36:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
36 | e(CLUSTER)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:41:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
41 | e(JOIN)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:49:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
49 | e(LINKAGE)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:63:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
63 | e(DISTANCE)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:70:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
70 | e(PPSCORE)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:79:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
79 | e(SEQWEIGHT)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:88:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
88 | e(OBJSCORE)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:10:
./enums.h:94:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
94 | e(TERMGAPS)
| ^
enumtostr.cpp:9:16: note: expanded from macro 'e'
9 | #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; }
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from enumtostr.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
397 | if (nB > 0)
| ^~~~~~
estring.cpp:409:11: note: uninitialized use occurs here
409 | switch (cType)
| ^~~~~
estring.cpp:397:4: note: remove the 'if' if its condition is always true
397 | if (nB > 0)
| ^~~~~~~~~~~
398 | {
399 | cType = 'I';
400 | ++nA;
401 | --nB;
402 | }
|
403 | else
| ~~~~
404 | assert(false);
| ~~~~~~~~~~~~~
estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
395 | else if (nA < 0)
| ^~~~~~
estring.cpp:409:11: note: uninitialized use occurs here
409 | switch (cType)
| ^~~~~
estring.cpp:395:8: note: remove the 'if' if its condition is always true
395 | else if (nA < 0)
| ^~~~~~~~~~~
396 | {
397 | if (nB > 0)
398 | {
399 | cType = 'I';
400 | ++nA;
401 | --nB;
402 | }
403 | else
404 | assert(false);
405 | }
|
406 | else
| ~~~~
407 | assert(false);
| ~~~~~~~~~~~~~
estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
386 | else if (nB < 0)
| ^~~~~~
estring.cpp:409:11: note: uninitialized use occurs here
409 | switch (cType)
| ^~~~~
estring.cpp:386:9: note: remove the 'if' if its condition is always true
386 | else if (nB < 0)
| ^~~~~~~~~~~
387 | {
388 | cType = 'D';
389 | --nA;
390 | ++nB;
391 | }
|
392 | else
| ~~~~
393 | assert(false);
| ~~~~~~~~~~~~~
estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning
377 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function]
464 | static bool CanMultiplyEstrings(const short es1[], const short es2[])
| ^~~~~~~~~~~~~~~~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fasta.cpp -o fasta.o
fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
15 | unsigned uSeqCount = 0;
| ^~~~~~~~~
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
16 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
235 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp:238:15: warning: unused variable 'pName1' [-Wunused-variable]
238 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function]
104 | static void ListCount(const unsigned char Count[])
| ^~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
223 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable]
33 | static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
| ^~~~~~~~~~~~~~~~~~
fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function]
85 | static void ListCount(const unsigned char Count[])
| ^~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function]
11 | static char *TupleToStr(int t)
| ^~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function]
12 | static char *TupleToStr(int t)
| ^~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignsimple.cpp -o glbalignsimple.o
glbalignsimple.cpp:24:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
24 | sprintf(str, "%6.1f", s);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from glbalignsimple.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function]
28 | static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
| ^~~~~~
glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function]
52 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
| ^~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
177 | const SCORE *ptrRowA = MxRowA[i];
| ^~~~~~~
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
119 | const unsigned uPrefixCountA = uLengthA + 1;
| ^~~~~~~~~~~~~
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
120 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function]
11 | static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
| ^~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp:19:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
19 | sprintf(str, "%6.3g", s);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch]
123 | switch (g_PPScore)
| ^~~~~~~~~
glbalndimer.cpp:123:10: note: add missing switch cases
123 | switch (g_PPScore)
| ^
124 | {
125 | case PPSCORE_LE:
126 | return ScoreProfPosDimerLE(PPA, PPB);
127 |
128 | case PPSCORE_SP:
129 | case PPSCORE_SV:
130 | return ScoreProfPosDimerPSP(PPA, PPB);
131 | }
In file included from glbalndimer.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
14 | static const char *LocalScoreToStr(SCORE s)
| ^~~~~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globals.cpp -o globals.o
globals.cpp:67:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations]
67 | vsprintf(szStr, szFormat, ArgList);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:199:1: note: 'vsprintf' has been explicitly marked deprecated here
199 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
globals.cpp:91:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations]
91 | vsprintf(szStr, szFormat, ArgList);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:199:1: note: 'vsprintf' has been explicitly marked deprecated here
199 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
globals.cpp:116:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations]
116 | vsprintf(szStr, szFormat, ArgList);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:199:1: note: 'vsprintf' has been explicitly marked deprecated here
199 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from globals.cpp:6:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalsosx.cpp -o globalsosx.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable]
137 | static SCORE Gonnet160[20][20] =
| ^~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gotowt.cpp -o gotowt.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intmath.cpp -o intmath.o
intmath.cpp:304:12: warning: variable 'uNumberGreater' set but not used [-Wunused-but-set-variable]
304 | unsigned uNumberGreater = 0;
| ^
intmath.cpp:328:12: warning: variable 'uNumberGreater' set but not used [-Wunused-but-set-variable]
328 | unsigned uNumberGreater = 0;
| ^
In file included from intmath.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
main.cpp:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
111 | NULL
| ^~~~
| { }
/Library/Developer/CommandLineTools/usr/lib/clang/16/include/__stddef_null.h:21:14: note: expanded from macro 'NULL'
21 | #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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
18 | const unsigned uSeqLength = s.Length();
| ^~~~~~~~~~
makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
94 | const PWPath &Path = Nodes[uNodeIndex].m_Path;
| ^~~~
makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
168 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function]
12 | static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
| ^~~~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msa.cpp -o msa.o
msa.cpp:397:3: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
397 | sprintf(szStr, "%u", u);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
msa.cpp:411:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
411 | sprintf(szStr, "%u", u);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from msa.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function]
385 | static void FmtChar(char c, unsigned uWidth)
| ^~~~~~~
msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function]
392 | static void FmtInt(unsigned u, unsigned uWidth)
| ^~~~~~
msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function]
407 | static void FmtInt0(unsigned u, unsigned uWidth)
| ^~~~~~~
msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function]
419 | static void FmtPad(unsigned n)
| ^~~~~~
7 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msa2.cpp -o msa2.o
msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
357 | switch (Method)
| ^~~~~~
msa2.cpp:357:10: note: add missing switch cases
357 | switch (Method)
| ^
358 | {
359 | case SEQWEIGHT_None:
msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
476 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function]
24 | static const char *strfind(const char *s, const char *t)
| ^~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwrec.cpp -o nwrec.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
390 | default:
| ^~~~~~~
nwsmall.cpp:394:14: note: uninitialized use occurs here
394 | TB[i][j] |= Bit;
| ^~~
nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning
378 | char Bit;
| ^
| = '\0'
nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
408 | default:
| ^~~~~~~
nwsmall.cpp:412:14: note: uninitialized use occurs here
412 | TB[i][j] |= Bit;
| ^~~
nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning
399 | char Bit;
| ^
| = '\0'
nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
426 | default:
| ^~~~~~~
nwsmall.cpp:430:14: note: uninitialized use occurs here
430 | TB[i][j] |= Bit;
| ^~~
nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning
417 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function]
397 | static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c)
| ^~~~~~~~~
nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function]
415 | static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c)
| ^~~~~~~~~
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
31 | switch (OS)
| ^~
objscore.cpp:31:10: note: add missing switch cases
31 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objscore2.cpp -o objscore2.o
objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
22 | switch (g_TermGaps)
| ^~~~~~~~~~
objscore2.cpp:22:10: note: add missing switch cases
22 | switch (g_TermGaps)
| ^
23 | {
24 | case TERMGAPS_Full:
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
62 | SCORE scoreGaps = 0;
| ^~~~~~~~~
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
63 | bool bGapping1 = false;
| ^~~~~~~~~
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
64 | bool bGapping2 = false;
| ^~~~~~~~~
objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
67 | bool bLeftTermGap = false;
| ^
objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
82 | bool bRightTermGap = false;
| ^
objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
140 | bool bLeftTermGap = false;
| ^
objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
155 | bool bRightTermGap = false;
| ^
objscore2.cpp:250:11: warning: variable 'uPairCount' set but not used [-Wunused-but-set-variable]
250 | unsigned uPairCount = 0;
| ^
objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
314 | const unsigned uColCount2 = msa2.GetColCount();
| ^~~~~~~~~~
objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
493 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optionsR.cpp -o optionsR.o
optionsR.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
21 | "in", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
22 | "in1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
23 | "in2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
24 | "out", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
25 | "MaxIters", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
26 | "MaxHours", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
27 | "GapOpen", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
28 | "GapOpen2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
29 | "GapExtend", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
30 | "GapExtend2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
31 | "GapAmbig", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
32 | "Center", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
33 | "SmoothScoreCeil", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
34 | "MinBestColScore", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
35 | "MinSmoothScore", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
36 | "ObjScore", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
37 | "SmoothWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
38 | "RefineWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
39 | "FromWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
40 | "ToWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
41 | "SaveWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
42 | "WindowOffset", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
43 | "FirstWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
44 | "AnchorSpacing", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
45 | "Log", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
46 | "LogA", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
47 | "MaxTrees", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
48 | "SUEFF", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
49 | "Distance", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
50 | "Distance1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
51 | "Distance2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
52 | "Weight", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
53 | "Weight1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
54 | "Weight2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
55 | "Cluster", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
56 | "Cluster1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
57 | "Cluster2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
58 | "Root1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
59 | "Root2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
60 | "Tree1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
61 | "Tree2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
62 | "UseTree", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
63 | "UseTree_NoWarn", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
64 | "DiagLength", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
65 | "DiagMargin", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
66 | "DiagBreak", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
67 | "Hydro", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
68 | "HydroFactor", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
69 | "SPScore", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
70 | "SeqType", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
71 | "MaxMB", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
72 | "ComputeWeights", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
73 | "MaxSubFam", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
74 | "ScoreFile", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
75 | "TermGaps", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
76 | "FASTAOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
77 | "CLWOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
78 | "CLWStrictOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
79 | "HTMLOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
80 | "MSFOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:81:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
81 | "PHYIOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:82:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
82 | "PHYSOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:83:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
83 | "Matrix", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:84:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
84 | "DistMx1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:85:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
85 | "DistMx2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:86:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
86 | "Weight", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
92 | "LE", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
93 | "SP", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
94 | "SV", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
95 | "SPN", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
96 | "Core", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
97 | "NoCore", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
98 | "Diags1", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
99 | "Diags2", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
100 | "Diags", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
101 | "Quiet", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
102 | "MSF", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
103 | "Verbose", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
104 | "Anchors", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
105 | "NoAnchors", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
106 | "Refine", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
107 | "RefineW", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
108 | "SW", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
109 | "Profile", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
110 | "PPScore", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
111 | "ClusterOnly", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
112 | "Brenner", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
113 | "Dimer", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
114 | "clw", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
115 | "clwstrict", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
116 | "HTML", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
117 | "Version", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
118 | "Stable", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
119 | "Group", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
120 | "FASTA", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
121 | "ProfDB", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
122 | "PAS", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
123 | "PHYI", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:124:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
124 | "PHYS", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:125:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
125 | "TomHydro", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
optionsR.cpp:126:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
126 | "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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
102 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:9:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
9 | 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]
10 | 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]
11 | 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]
12 | 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]
13 | -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]
14 | 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]
15 | -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]
16 | 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]
17 | -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]
18 | -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]
19 | 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]
20 | 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]
21 | 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]
22 | -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]
23 | -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]
24 | 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]
25 | 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]
26 | 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]
27 | -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]
28 | -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]
29 | 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]
30 | 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]
31 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable]
6 | static float PAM200[23][23] =
| ^~~~~~
25 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c params.cpp -o params.o
params.cpp:445:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
445 | switch (g_PPScore)
| ^~~~~~~~~
params.cpp:445:10: note: add missing switch cases
445 | switch (g_PPScore)
| ^
446 | {
447 | case PPSCORE_LE:
params.cpp:652:14: warning: unused variable 'VTML_LA' [-Wunused-variable]
652 | SCOREMATRIX VTML_LA;
| ^~~~~~~
params.cpp:653:14: warning: unused variable 'PAM200' [-Wunused-variable]
653 | SCOREMATRIX PAM200;
| ^~~~~~
params.cpp:654:14: warning: unused variable 'PAM200NoCenter' [-Wunused-variable]
654 | SCOREMATRIX PAM200NoCenter;
| ^~~~~~~~~~~~~~
params.cpp:655:14: warning: unused variable 'VTML_SP' [-Wunused-variable]
655 | SCOREMATRIX VTML_SP;
| ^~~~~~~
params.cpp:656:14: warning: unused variable 'VTML_SPNoCenter' [-Wunused-variable]
656 | SCOREMATRIX VTML_SPNoCenter;
| ^~~~~~~~~~~~~~~
params.cpp:657:14: warning: unused variable 'NUC_SP' [-Wunused-variable]
657 | SCOREMATRIX NUC_SP;
| ^~~~~~
params.cpp:659:2: warning: expression result unused [-Wunused-value]
659 | g_ptrScoreMatrix;
| ^~~~~~~~~~~~~~~~
In file included from params.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy.cpp -o phy.o
phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
665 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy3.cpp -o phy3.o
phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
125 | const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
| ^~~~~~~~~
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
167 | const unsigned uLeafCount = tree.GetLeafCount();
| ^~~~~~~~~~
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
190 | double dAllMaxDist = -1e20;
| ^~~~~~~~~~~
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
191 | unsigned uMaxFrom = NULL_NEIGHBOR;
| ^~~~~~~~
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
192 | unsigned uMaxTo = NULL_NEIGHBOR;
| ^~~~~~
phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
263 | unsigned uMostDistantLeaf = 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function]
45 | static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
| ^~~~~~~
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy4.cpp -o phy4.o
phy4.cpp:242:3: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
242 | sprintf(szName, "Subfam_%u", uSubfamIndex + 1);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from phy4.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
22 | switch(m_Distance)
| ^~~~~~~~~~
./msadist.h:22:10: note: add missing switch cases
22 | switch(m_Distance)
| ^
23 | {
24 | case DISTANCE_PctIdKimura:
25 | return KimuraDist(dPctId);
26 | case DISTANCE_PctIdLog:
27 | if (dPctId < 0.05)
28 | dPctId = 0.05;
29 | return -log(dPctId);
30 | }
In file included from profdb.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp:20:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
20 | sprintf(str, "%5.1f", s);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
230 | switch (g_Alpha)
| ^~~~~~~
profilefrommsa.cpp:230:10: note: add missing switch cases
230 | switch (g_Alpha)
| ^
231 | {
232 | case ALPHA_Amino:
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
245 | const unsigned uSeqCount = a.GetSeqCount();
| ^~~~~~~~~
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
253 | unsigned uHydrophobicRunLength = 0;
| ^~~~~~~~~~~~~~~~~~~~~
In file included from profilefrommsa.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
15 | static const char *LocalScoreToStr(SCORE s)
| ^~~~~~~~~~~~~~~
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progalign.cpp -o progalign.o
progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
41 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progress.cpp -o progress.o
progress.cpp:114:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations]
114 | vsprintf(szStr, szFormat, ArgList);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:199:1: note: 'vsprintf' has been explicitly marked deprecated here
199 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from progress.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwpath.cpp -o pwpath.o
pwpath.cpp:79:16: warning: unused variable 'LastEdge' [-Wunused-variable]
79 | const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
| ^~~~~~~~
pwpath.cpp:80:11: warning: variable 'uStartA' set but not used [-Wunused-but-set-variable]
80 | unsigned uStartA = FirstEdge.uPrefixLengthA;
| ^
pwpath.cpp:81:11: warning: variable 'uStartB' set but not used [-Wunused-but-set-variable]
81 | unsigned uStartB = FirstEdge.uPrefixLengthB;
| ^
pwpath.cpp:212:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
212 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function]
30 | static unsigned MxCharToLetter(char c)
| ^~~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c realigndiffse.cpp -o realigndiffse.o
realigndiffse.cpp:72:13: warning: unused variable 'uNewRight' [-Wunused-variable]
72 | unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
| ^~~~~~~~~
realigndiffse.cpp:75:13: warning: unused variable 'uOldRight' [-Wunused-variable]
75 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
22 | switch(m_Distance)
| ^~~~~~~~~~
./msadist.h:22:10: note: add missing switch cases
22 | switch(m_Distance)
| ^
23 | {
24 | case DISTANCE_PctIdKimura:
25 | return KimuraDist(dPctId);
26 | case DISTANCE_PctIdLog:
27 | if (dPctId < 0.05)
28 | dPctId = 0.05;
29 | return -log(dPctId);
30 | }
In file included from refine.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
256 | default:
| ^~~~~~~
refinehoriz.cpp:259:56: note: uninitialized use occurs here
259 | RefineHeightParts(msaIn, tree, Internals, bReverse, bRight,
| ^~~~~~
refinehoriz.cpp:247:15: note: initialize the variable 'bRight' to silence this warning
247 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
63 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinew.cpp -o refinew.o
refinew.cpp:26:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
26 | const unsigned uColCountCat = uColCount1 + uColCount2;
| ^~~~~~~~~~~~
refinew.cpp:134:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
134 | sprintf(fn, "win%d_inaln.tmp", uWindowIndex);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
refinew.cpp:138:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
138 | sprintf(fn, "win%d_inseqs.tmp", uWindowIndex);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
refinew.cpp:142:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
142 | sprintf(fn, "win%d_outaln.tmp", uWindowIndex);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
refinew.cpp:129:13: warning: unused variable 'uOutCols' [-Wunused-variable]
129 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable]
17 | static const double Dayhoff_CalibrationFactor = 1.3370;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable]
19 | static const double MV_CalibrationFactor = 1.1775;
| ^~~~~~~~~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function]
37 | static void FreeGapInfo(GAPINFO *GI)
| ^~~~~~~~~~~
scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function]
80 | static SCORE Penalty(unsigned Length, bool Term)
| ^~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
201 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable]
6 | const size_t MAX_FASTA_LINE = 16000;
| ^~~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spfast.cpp -o spfast.o
spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
252 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function]
14 | static const char *GapTypeToStr(int GapType)
| ^~~~~~~~~~~~
spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function]
59 | static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
| ^~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subfam.cpp -o subfam.o
subfam.cpp:171:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
171 | sprintf(CmdLine, "probcons %s > %s 2> /dev/null", InTmp, OutTmp);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
173 | int NotUsed = system(CmdLine);
| ^~~~~~~
subfam.cpp:243:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
243 | sprintf(NewFileName, "%s/%s", Path, FileName);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from subfam.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subfams.cpp -o subfams.o
In file included from subfams.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
subfams.cpp:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function]
10 | static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
| ^~~~~~~~~~~~~~~~~~
subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function]
40 | static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
| ^~~~~~~~~~~~~~~~~~~~~~
subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function]
52 | static void Relax(DistFunc &DF, unsigned u, unsigned v)
| ^~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sw.cpp -o sw.o
sw.cpp:16:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
16 | sprintf(str, "%6.2f", s);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from sw.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function]
20 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
| ^~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c textfile.cpp -o textfile.o
textfile.cpp:104:6: warning: unused variable 'i' [-Wunused-variable]
104 | int i = fputc(c, m_ptrFile);
| ^
textfile.cpp:117:6: warning: unused variable 'iError' [-Wunused-variable]
117 | int iError = fputs(szLine, m_ptrFile);
| ^~~~~~
textfile.cpp:126:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations]
126 | vsprintf(szStr, szFormat, ArgList);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:199:1: note: 'vsprintf' has been explicitly marked deprecated here
199 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from textfile.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c traceback.cpp -o traceback.o
traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
21 | const unsigned uPrefixCountB = uLengthB + 1;
| ^~~~~~~~~~~~~
traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
195 | default:
| ^~~~~~~
traceback.cpp:202:15: note: uninitialized use occurs here
202 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
186 | else if (EQ(Score, scoreSI))
| ^~~~~~~~~~~~~~~~~~
traceback.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
traceback.cpp:202:15: note: uninitialized use occurs here
202 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
traceback.cpp:186:9: note: remove the 'if' if its condition is always true
186 | else if (EQ(Score, scoreSI))
| ^~~~~~~~~~~~~~~~~~~~~~~
187 | cPrevEdgeType = 'S';
| ~
188 | else
| ~~~~
189 | Quit("TraceBack: failed to match I");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
150 | else if (EQ(Score, scoreSD))
| ^~~~~~~~~~~~~~~~~~
traceback.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
traceback.cpp:202:15: note: uninitialized use occurs here
202 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
traceback.cpp:150:9: note: remove the 'if' if its condition is always true
150 | else if (EQ(Score, scoreSD))
| ^~~~~~~~~~~~~~~~~~~~~~~
151 | cPrevEdgeType = 'S';
| ~
152 | else
| ~~~~
153 | Quit("TraceBack: failed to match D");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
112 | else if (EQ(scoreSM, Score))
| ^~~~~~~~~~~~~~~~~~
traceback.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
traceback.cpp:202:15: note: uninitialized use occurs here
202 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
traceback.cpp:112:9: note: remove the 'if' if its condition is always true
112 | else if (EQ(scoreSM, Score))
| ^~~~~~~~~~~~~~~~~~~~~~~
113 | cPrevEdgeType = 'S';
| ~
114 | else
| ~~~~
115 | Quit("TraceBack: failed to match M score=%g M=%g D=%g I=%g S=%g",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
116 | Score, scoreMM, scoreDM, scoreIM, scoreSM);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
68 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracebacksw.cpp -o tracebacksw.o
tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
22 | const unsigned uPrefixCountB = uLengthB + 1;
| ^~~~~~~~~~~~~
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
29 | SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
| ^~~~~~~~
tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
175 | default:
| ^~~~~~~
tracebacksw.cpp:182:15: note: uninitialized use occurs here
182 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
166 | else if (EQ(Score, scoreSI))
| ^~~~~~~~~~~~~~~~~~
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
tracebacksw.cpp:182:15: note: uninitialized use occurs here
182 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true
166 | else if (EQ(Score, scoreSI))
| ^~~~~~~~~~~~~~~~~~~~~~~
167 | cPrevEdgeType = 'S';
| ~
168 | else
| ~~~~
169 | Quit("TraceBack2: failed to match I");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
130 | else if (EQ(Score, scoreSD))
| ^~~~~~~~~~~~~~~~~~
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
tracebacksw.cpp:182:15: note: uninitialized use occurs here
182 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true
130 | else if (EQ(Score, scoreSD))
| ^~~~~~~~~~~~~~~~~~~~~~~
131 | cPrevEdgeType = 'S';
| ~
132 | else
| ~~~~
133 | Quit("TraceBack2: failed to match D");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
92 | else if (EQ(scoreMatch, Score))
| ^~~~~~~~~~~~~~~~~~~~~
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
tracebacksw.cpp:182:15: note: uninitialized use occurs here
182 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true
92 | else if (EQ(scoreMatch, Score))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
93 | cPrevEdgeType = 'S';
| ~
94 | else
| ~~~~
95 | Quit("TraceBack2: failed to match M score=%g M=%g D=%g I=%g S=%g",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | Score, scoreMM, scoreDM, scoreIM, scoreSM);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
43 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
7 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
22 | switch(m_Distance)
| ^~~~~~~~~~
./msadist.h:22:10: note: add missing switch cases
22 | switch(m_Distance)
| ^
23 | {
24 | case DISTANCE_PctIdKimura:
25 | return KimuraDist(dPctId);
26 | case DISTANCE_PctIdLog:
27 | if (dPctId < 0.05)
28 | dPctId = 0.05;
29 | return -log(dPctId);
30 | }
In file included from treefrommsa.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c typetostr.cpp -o typetostr.o
typetostr.cpp:13:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
typetostr.cpp:34:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
34 | sprintf(pStr, "%8g", Score);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
typetostr.cpp:51:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
51 | sprintf(pStr, "%.3g", Score);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
In file included from typetostr.cpp:1:
In file included from ./muscle.h:34:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
272 | default:
| ^~~~~~~
upgma2.cpp:292:17: note: uninitialized use occurs here
292 | g_Dist[vL] = dtNewDist;
| ^~~~~~~~~
upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning
252 | dist_t dtNewDist;
| ^
| = 0.0
upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
366 | 0, 2, 14, 14, 20,
| ^~~~~~~~~~~~~~~~~
| { }
upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
367 | 2, 0, 14, 14, 20,
| ^~~~~~~~~~~~~~~~~
| { }
upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
368 | 14, 14, 0, 4, 20,
| ^~~~~~~~~~~~~~~~~~
| { }
upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
369 | 14, 14, 4, 0, 20,
| ^~~~~~~~~~~~~~~~~~
| { }
upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
370 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function]
68 | static void ListState()
| ^~~~~~~~~
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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]
37 | default:
| ^~~~~~~
writescorefile.cpp:40:12: note: uninitialized use occurs here
40 | dSum += Score;
| ^~~~~
writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning
27 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-muscle/00new/muscle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (muscle)
