OSX binary not working about muscle HOT 4 CLOSED

Yikes, sorry but no idea why you would get an error like that. Can you try re-building from source? There is a Makefile_osx under src/.

from muscle.

Thanks for responding, here are the errors when trying to build.
make -f Makefile_osx
g++ -fopenmp -ffast-math -msse -mfpmath=sse -O3 -DNDEBUG -c -o o/addconfseq.o addconfseq.cpp
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:221:1: error: reference to 'byte' is ambiguous
221 | byte *ReadAllStdioFile32(FILE *f, uint32 &FileSize);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
myutils.h:222:1: error: reference to 'byte' is ambiguous
222 | byte *ReadAllStdioFile64(FILE *f, uint64 &FileSize);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
myutils.h:224:1: error: reference to 'byte' is ambiguous
224 | byte *ReadAllStdioFile(FILE *f, uint32 &FileSize);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
myutils.h:225:1: error: reference to 'byte' is ambiguous
225 | byte *ReadAllStdioFile64(FILE *f, uint64 &FileSize);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
myutils.h:227:1: error: reference to 'byte' is ambiguous
227 | byte *ReadAllStdioFile32(const string &FileName, uint32 &FileSize);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
myutils.h:228:1: error: reference to 'byte' is ambiguous
228 | byte *ReadAllStdioFile64(const string &FileName, uint64 &FileSize);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:434:32: error: reference to 'byte' is ambiguous
434 | void SeqToFasta(FILE *f, const byte *Seq, unsigned L, const char *Label);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:435:32: error: reference to 'byte' is ambiguous
435 | void SeqToFastq(FILE *f, const byte *Seq, unsigned L, const char *Qual, const char *Label);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:436:34: error: reference to 'byte' is ambiguous
436 | void SeqToFastaRC(FILE *f, const byte *Seq, unsigned L, const char *Label);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:437:23: error: reference to 'byte' is ambiguous
437 | void RevCompSeq(const byte *Seq, unsigned L, byte *RCSeq);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:437:46: error: reference to 'byte' is ambiguous
437 | void RevCompSeq(const byte *Seq, unsigned L, byte *RCSeq);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:437:46: error: 'byte' has not been declared
437 | void RevCompSeq(const byte *Seq, unsigned L, byte *RCSeq);
| ^~~~
myutils.h:444:23: error: 'char mytoupper' redeclared as different kind of entity
444 | inline char mytoupper(byte c) { return c & (~0x20); }
| ^~~~
myutils.h:443:13: note: previous declaration 'char mytoupper(char)'
443 | inline char mytoupper(char c) { return c & (~0x20); }
| ^~~~~~~~~
myutils.h:444:23: error: reference to 'byte' is ambiguous
444 | inline char mytoupper(byte c) { return c & (~0x20); }
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:445:23: error: reference to 'byte' is ambiguous
445 | inline bool myislower(byte c) { return (c & 0x20) != 0; }
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:446:29: error: 'bool myislower(char)' redeclared as different kind of entity
446 | inline bool myislower(char c) { return (c & 0x20) != 0; }
| ^
myutils.h:445:13: note: previous declaration 'bool myislower'
445 | inline bool myislower(byte c) { return (c & 0x20) != 0; }
| ^~~~~~~~~
In file included from multisequence.h:4,
from muscle.h:23,
from addconfseq.cpp:1:
sequence.h:86:15: error: reference to 'byte' is ambiguous
86 | const byte *GetBytePtr() const
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:23,
from addconfseq.cpp:1:
multisequence.h:110:15: error: reference to 'byte' is ambiguous
110 | const byte *GetByteSeq(uint SeqIndex, uint &L) const
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:23,
from addconfseq.cpp:1:
multisequence.h:118:15: error: reference to 'byte' is ambiguous
118 | const byte *GetBytePtr(uint SeqIndex) const
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:25,
from addconfseq.cpp:1:
mysparsemx.h:14:9: error: reference to 'byte' is ambiguous
14 | byte *m_ValueVec = 0;
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:25,
from addconfseq.cpp:1:
mysparsemx.h:19:15: error: reference to 'byte' is ambiguous
19 | const byte *m_X = 0;
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:25,
from addconfseq.cpp:1:
mysparsemx.h:20:15: error: reference to 'byte' is ambiguous
20 | const byte *m_Y = 0;
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:25,
from addconfseq.cpp:1:
mysparsemx.h: In constructor 'MySparseMx::MySparseMx()':
mysparsemx.h:30:17: error: 'm_ValueVec' was not declared in this scope
30 | m_ValueVec = 0;
| ^~~~~~~~~~
mysparsemx.h:35:17: error: 'm_X' was not declared in this scope; did you mean 'm_LX'?
35 | m_X = 0;
| ^~~
| m_LX
mysparsemx.h:36:17: error: 'm_Y' was not declared in this scope; did you mean 'm_LY'?
36 | m_Y = 0;
| ^~~
| m_LY
mysparsemx.h: In member function 'void MySparseMx::Clear()':
mysparsemx.h:45:24: error: 'm_ValueVec' was not declared in this scope
45 | myfree(m_ValueVec);
| ^~~~~~~~~~
mysparsemx.h: In member function 'float MySparseMx::GetProb_Offset(uint) const':
mysparsemx.h:58:49: error: 'm_ValueVec' was not declared in this scope
58 | const float *ptr_P = (float ) (m_ValueVec + 8Offset);
| ^~~~~~~~~~
mysparsemx.h: In member function 'uint MySparseMx::GetCol_Offset(uint) const':
mysparsemx.h:65:47: error: 'm_ValueVec' was not declared in this scope
65 | const uint *ptr_j = (uint ) (m_ValueVec + 8Offset + 4);
| ^~~~~~~~~~
mysparsemx.h: In member function 'void MySparseMx::SetProb_Offset(uint, float)':
mysparsemx.h:72:43: error: 'm_ValueVec' was not declared in this scope
72 | float *ptr_P = (float ) (m_ValueVec + 8Offset);
| ^~~~~~~~~~
mysparsemx.h: In member function 'void MySparseMx::SetCol_Offset(uint, uint) const':
mysparsemx.h:78:41: error: 'm_ValueVec' was not declared in this scope
78 | uint *ptr_j = (uint ) (m_ValueVec + 8Offset + 4);
| ^~~~~~~~~~
In file included from muscle.h:29,
from addconfseq.cpp:1:
alpha.h: At global scope:
alpha.h:118:8: error: reference to 'byte' is ambiguous
118 | extern byte g_CharToLetterNucleo[256];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:29,
from addconfseq.cpp:1:
alpha.h:119:8: error: reference to 'byte' is ambiguous
119 | extern byte g_CharToLetterAmino[256];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:31,
from addconfseq.cpp:1:
mpcflat.h:70:15: error: reference to 'byte' is ambiguous
70 | const byte *GetBytePtr(uint SeqIndex) const;
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:31,
from addconfseq.cpp:1:
mpcflat.h:87:24: error: reference to 'byte' is ambiguous
87 | void CalcFwdFlat(const byte *X, uint LX, const byte *Y, uint LY, float *Flat);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:31,
from addconfseq.cpp:1:
mpcflat.h:87:48: error: reference to 'byte' is ambiguous
87 | void CalcFwdFlat(const byte *X, uint LX, const byte *Y, uint LY, float *Flat);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:31,
from addconfseq.cpp:1:
mpcflat.h:88:24: error: reference to 'byte' is ambiguous
88 | void CalcBwdFlat(const byte *X, uint LX, const byte *Y, uint LY, float *Flat);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:31,
from addconfseq.cpp:1:
mpcflat.h:88:48: error: reference to 'byte' is ambiguous
88 | void CalcBwdFlat(const byte *X, uint LX, const byte *Y, uint LY, float *Flat);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:32,
from addconfseq.cpp:1:
kmerscan.h:4:26: error: reference to 'byte' is ambiguous
4 | void SyncmerScanNt(const byte *Seq, uint Lo, uint Len, uint k, uint d,
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:32,
from addconfseq.cpp:1:
kmerscan.h:6:26: error: reference to 'byte' is ambiguous
6 | void SyncmerScanAa(const byte *Seq, uint Lo, uint Len, uint k, uint d,
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:32,
from addconfseq.cpp:1:
kmerscan.h:15:26: error: reference to 'byte' is ambiguous
15 | uint32 SeqToCodeNt(const byte *Seq, uint k);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:32,
from addconfseq.cpp:1:
kmerscan.h:16:26: error: reference to 'byte' is ambiguous
16 | uint32 SeqToCodeAa(const byte *Seq, uint k);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:32,
from addconfseq.cpp:1:
kmerscan.h:17:37: error: reference to 'byte' is ambiguous
17 | uint32 SeqToCode(bool Nucleo, const byte *Seq, uint k);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:9:7: error: reference to 'byte' is ambiguous
9 | const byte INVALID_LETTER = 0xff;
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:10:7: error: reference to 'byte' is ambiguous
10 | const byte INVALID_CHAR = '?';
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:13:8: error: reference to 'byte' is ambiguous
13 | extern byte g_AminoAcidChars[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:14:8: error: reference to 'byte' is ambiguous
14 | extern byte g_CharToLetterAmino[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:15:8: error: reference to 'byte' is ambiguous
15 | extern byte g_CharToLetterAminoStop[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:16:8: error: reference to 'byte' is ambiguous
16 | extern byte g_CharToLetterAminoGap[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:17:8: error: reference to 'byte' is ambiguous
17 | extern byte g_LetterToCharAmino[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:18:8: error: reference to 'byte' is ambiguous
18 | extern byte g_LetterToCharAminoGap[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:19:8: error: reference to 'byte' is ambiguous
19 | extern byte g_CharToLetterNucleo[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:20:8: error: reference to 'byte' is ambiguous
20 | extern byte g_CharToLetterNucleoGap[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:21:8: error: reference to 'byte' is ambiguous
21 | extern byte g_CharToLetterNucleoMasked[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:22:8: error: reference to 'byte' is ambiguous
22 | extern byte g_LetterToCharNucleo[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:23:8: error: reference to 'byte' is ambiguous
23 | extern byte g_LetterToCharNucleoGap[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:24:8: error: reference to 'byte' is ambiguous
24 | extern byte g_CodonWordToAminoLetter[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:25:8: error: reference to 'byte' is ambiguous
25 | extern byte g_CodonWordToAminoChar[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:26:8: error: reference to 'byte' is ambiguous
26 | extern byte g_CharToCompChar[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:27:8: error: reference to 'byte' is ambiguous
27 | extern byte g_CharToCompLetter[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:28:8: error: reference to 'byte' is ambiguous
28 | extern byte g_IUPAC_PairCharToChar1[256];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:29:8: error: reference to 'byte' is ambiguous
29 | extern byte g_IUPAC_PairCharToChar2[256];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:30:8: error: reference to 'byte' is ambiguous
30 | extern byte g_IUPAC_PairCharToCharCase[256];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:31:8: error: reference to 'byte' is ambiguous
31 | extern byte g_CharToLetterSEB8[256];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:43:8: error: reference to 'byte' is ambiguous
43 | extern byte g_LetterToCharRed[];
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:48:1: error: reference to 'byte' is ambiguous
48 | byte GetAminoCharFrom3NucChars(byte c1, byte c2,
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:56:26: error: 'bool isgap' redeclared as different kind of entity
56 | static inline bool isgap(byte c)
| ^~~~
In file included from muscle.h:29,
from addconfseq.cpp:1:
alpha.h:113:20: note: previous declaration 'bool isgap(char)'
113 | static inline bool isgap(char c)
| ^~~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:56:26: error: reference to 'byte' is ambiguous
56 | static inline bool isgap(byte c)
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from muscle.h:33,
from addconfseq.cpp:1:
alpha3.h:62:1: error: reference to 'byte' is ambiguous
62 | byte IUPAC_Pair(byte CharOrWildcard1, byte CharOrWildcard2);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from addconfseq.cpp:1:
muscle.h:110:24: error: reference to 'byte' is ambiguous
110 | void CalcFwdFlat(const byte *X, uint LX, const byte *Y, uint LY, float *Flat);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from addconfseq.cpp:1:
muscle.h:110:48: error: reference to 'byte' is ambiguous
110 | void CalcFwdFlat(const byte *X, uint LX, const byte *Y, uint LY, float *Flat);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from addconfseq.cpp:1:
muscle.h:111:24: error: reference to 'byte' is ambiguous
111 | void CalcBwdFlat(const byte *X, uint LX, const byte *Y, uint LY, float *Flat);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
In file included from addconfseq.cpp:1:
muscle.h:111:48: error: reference to 'byte' is ambiguous
111 | void CalcBwdFlat(const byte *X, uint LX, const byte *Y, uint LY, float *Flat);
| ^~~~
In file included from /opt/local/include/gcc11/c++/bits/stl_algobase.h:61,
from /opt/local/include/gcc11/c++/bits/char_traits.h:39,
from /opt/local/include/gcc11/c++/string:40,
from myutils.h:22,
from muscle.h:21,
from addconfseq.cpp:1:
/opt/local/include/gcc11/c++/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
404 | enum class byte : unsigned char;
| ^~~~
In file included from muscle.h:21,
from addconfseq.cpp:1:
myutils.h:73:23: note: 'typedef unsigned char byte'
73 | typedef unsigned char byte;
| ^~~~
make: *** [o/addconfseq.o] Error 1

from muscle.

This is same as issue #4, it doesn't compile with gcc v11 which I'm working on, it seems to work with gcc v8 or v9 (not sure about v10).

from muscle.

Fixed in v5.1.

from muscle.