Comments (4)
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.
Related Issues (20)
- how to use it in .net core? any one who can help me? thank you!
- *** Error in `muscle': double free or corruption (out): 0x00007ffdb8176090 *** HOT 2
- Resampling Clarification HOT 5
- Can muscle be made to take two or more non-file cli arguments (input streams)? [v3.8] HOT 1
- Memory Object >4Gb error HOT 6
- gap penlty HOT 2
- @ in output filename required for -perm all with -super5 HOT 1
- Memory Object Too Large due to very long sequences HOT 2
- Automatic optimal number of threads HOT 2
- If is possible to release Muscle V5 version which has no dependence of omp.h? HOT 8
- Specifying threads HOT 4
- usorter.cpp(88) assert failed: L >= m_WordLength HOT 2
- Segmentation fault (core dumped)riors HOT 2
- Segmentation fault : only a few small sequences to align HOT 1
- alignment error when short sequence HOT 5
- Running time for large numbers of sequences
- python version of the code? HOT 1
- Fatal error: allocflat.cpp(15) assert failed: uint64(Size) == Size64 HOT 1
- segmentation fault muscle -align testing.fa -output alignment.afa HOT 3
- Error in `muscle': free(): invalid next size (normal): 0x00002b09305f4a40 ***
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from muscle.