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Created May 27, 2021 06:36
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errorlog
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gistfile1.txt
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/profile.h:24:11: note: in expansion of macro 'cs'
24 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/profile.h:68:39: error: 'Vector' does not name a type
68 | void Normalize(Profile<Abc>& p, const Vector<double>& norm, bool incl_any = false);
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/profile.h:68:45: error: expected ',' or '...' before '<' token
68 | void Normalize(Profile<Abc>& p, const Vector<double>& norm, bool incl_any = false);
| ^
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h:26:11: note: in expansion of macro 'cs'
26 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h: In function 'void Normalize(Profile<Abc>&, double, bool)':
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h:180:31: error: 'kNormalize' was not declared in this scope; did you mean 'Normalize'?
180 | if (fabs(val - sum) > kNormalize && sum != 0.0) {
| ^~~~~~~~~~
| Normalize
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h: At global scope:
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h:190:46: error: 'Vector' does not name a type
190 | inline void Normalize(Profile<Abc>& p, const Vector<double>& norm, bool incl_any) {
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h:190:52: error: expected ',' or '...' before '<' token
190 | inline void Normalize(Profile<Abc>& p, const Vector<double>& norm, bool incl_any) {
| ^
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h: In function 'void Normalize(Profile<Abc>&, int)':
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h:191:29: error: 'incl_any' was not declared in this scope
191 | const size_t abc_size = incl_any ? Abc::kSizeAny : Abc::kSize;
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h:195:18: error: 'norm' was not declared in this scope; did you mean 'std::norm'?
195 | if (fabs(norm[i] - sum) > kNormalize && sum != 0.0) {
| ^~~~
| std::norm
In file included from /usr/local/include/cs.h:34,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/usr/local/Cellar/gcc@10/10.3.0/include/c++/10.3.0/complex:1866:5: note: 'std::norm' declared here
1866 | norm(_Tp __x)
| ^~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/profile-inl.h:195:35: error: 'kNormalize' was not declared in this scope; did you mean 'Normalize'?
195 | if (fabs(norm[i] - sum) > kNormalize && sum != 0.0) {
| ^~~~~~~~~~
| Normalize
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/sequence.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/sequence.h:26:11: note: in expansion of macro 'cs'
26 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/globals.h:25:11: note: in expansion of macro 'cs'
25 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/alignment.h:31:11: note: in expansion of macro 'cs'
31 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/substitution_matrix.h:23:11: note: in expansion of macro 'cs'
23 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/log.h:29:11: note: in expansion of macro 'cs'
29 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/utils.h:35:11: note: in expansion of macro 'cs'
35 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/substitution_matrix-inl.h:27:11: note: in expansion of macro 'cs'
27 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:29:11: note: in expansion of macro 'cs'
29 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/assert_helpers.h:25:11: note: in expansion of macro 'cs'
25 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/io.h:35:11: note: in expansion of macro 'cs'
35 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/sequence-inl.h:26,
from /Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/io.h: In function 'bool StreamStartsWith(FILE*, const char*)':
/Users/mac/lab/guo/hh-suite/src/cs/io.h:185:14: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
185 | while (cs::fgetline(buffer, KB, fp)) if (strscn(buffer)) break;
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/as.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/as.h:23:11: note: in expansion of macro 'cs'
23 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/sequence-inl.h:29:11: note: in expansion of macro 'cs'
29 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/sequence-inl.h: In member function 'void Sequence<Abc>::Read(FILE*)':
/Users/mac/lab/guo/hh-suite/src/cs/sequence-inl.h:119:16: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
119 | while (cs::fgetline(buffer, kBuffSize, fin)) {
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/sequence-inl.h:129:16: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
129 | while (cs::fgetline(buffer, kBuffSize, fin) && !(buffer[0] == '/' && buffer[1] == '/')) {
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:27:11: note: in expansion of macro 'cs'
27 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h: In member function 'void Alignment<Abc>::ReadFastaFlavors(FILE*, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&)':
/Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:168:20: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
168 | while (cs::fgetline(buffer, kBufferSize, fin)) {
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:179:25: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
179 | cs::fgetline(buffer, kBufferSize, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:193:20: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
193 | while (cs::fgetline(buffer, kBufferSize, fin)) {
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h: In member function 'void Alignment<Abc>::ReadPsi(FILE*, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&)':
/Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:222:16: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
222 | while (cs::fgetline(buffer, kBufferSize, fin)) {
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:29:11: note: in expansion of macro 'cs'
29 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h: In member function 'void CountProfile<Abc>::Read(FILE*)':
/Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:68:7: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
68 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:71:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
71 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:74:7: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
74 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:87:7: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
87 | cs::fgetline(buffer, KB, fin); // skip alphabet description line
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:88:14: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
88 | while (cs::fgetline(buffer, KB, fin) && buffer[0] != '/' && buffer[1] != '/') {
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/profile_column.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/profile_column.h:23:11: note: in expansion of macro 'cs'
23 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:27:11: note: in expansion of macro 'cs'
27 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:26:11: note: in expansion of macro 'cs'
26 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts-inl.h:24:11: note: in expansion of macro 'cs'
24 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_library.h:26:11: note: in expansion of macro 'cs'
26 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/emission.h:28:11: note: in expansion of macro 'cs'
28 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:25:11: note: in expansion of macro 'cs'
25 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/context_library-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/library_pseudocounts.h:28,
from /Users/mac/lab/guo/hh-suite/src/cs/library_pseudocounts-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:39,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h: In member function 'void ContextProfile<Abc>::Read(FILE*)':
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:87:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
87 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:90:13: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
90 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:93:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
93 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:98:13: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
98 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:101:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
101 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:103:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
103 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:118:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
118 | cs::fgetline(buffer, KB, fin); // skip alphabet description line
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_profile-inl.h:119:16: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
119 | while (cs::fgetline(buffer, KB, fin) && buffer[0] != '/' && buffer[1] != '/') {
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/ran.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/ran.h:27:11: note: in expansion of macro 'cs'
27 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_library-inl.h:28:11: note: in expansion of macro 'cs'
28 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/library_pseudocounts.h:28,
from /Users/mac/lab/guo/hh-suite/src/cs/library_pseudocounts-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:39,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/context_library-inl.h: In member function 'void ContextLibrary<Abc>::Read(FILE*)':
/Users/mac/lab/guo/hh-suite/src/cs/context_library-inl.h:55:11: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
55 | if (cs::fgetline(buffer, KB, fin))
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/context_library-inl.h:57:11: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
57 | if (cs::fgetline(buffer, KB, fin))
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/library_pseudocounts.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/library_pseudocounts.h:30:11: note: in expansion of macro 'cs'
30 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/library_pseudocounts-inl.h:25:11: note: in expansion of macro 'cs'
25 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_state.h:28:11: note: in expansion of macro 'cs'
28 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf.h:30:11: note: in expansion of macro 'cs'
30 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_state-inl.h:25:11: note: in expansion of macro 'cs'
25 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/crf-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/crf_pseudocounts.h:28,
from /Users/mac/lab/guo/hh-suite/src/cs/crf_pseudocounts-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:40,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/crf_state-inl.h: In member function 'void CrfState<Abc>::Read(FILE*)':
/Users/mac/lab/guo/hh-suite/src/cs/crf_state-inl.h:34:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
34 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_state-inl.h:37:13: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
37 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_state-inl.h:40:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
40 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_state-inl.h:42:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
42 | cs::fgetline(buffer, KB, fin);
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_state-inl.h:55:9: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
55 | cs::fgetline(buffer, KB, fin); // skip alphabet description line
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_state-inl.h:56:16: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
56 | while (cs::fgetline(buffer, KB, fin) && buffer[0] != '/' && buffer[1] != '/') {
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/crf-inl.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf-inl.h:28:11: note: in expansion of macro 'cs'
28 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/crf_pseudocounts.h:28,
from /Users/mac/lab/guo/hh-suite/src/cs/crf_pseudocounts-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:40,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/crf-inl.h: In member function 'void Crf<Abc>::Read(FILE*)':
/Users/mac/lab/guo/hh-suite/src/cs/crf-inl.h:61:13: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
61 | if (cs::fgetline(buffer, KB, fin))
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf-inl.h:63:13: error: 'fgetline' is not a member of 'cs_di' {aka 'cs_di_sparse'}
63 | if (cs::fgetline(buffer, KB, fin))
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:37,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/crf_pseudocounts.h: At global scope:
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_pseudocounts.h:30:11: note: in expansion of macro 'cs'
30 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/crf_pseudocounts-inl.h:25:11: note: in expansion of macro 'cs'
25 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
/usr/local/include/cs.h:637:12: error: 'namespace cs_di { }' redeclared as different kind of entity
637 | #define cs cs_di
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/aa.h:26:11: note: in expansion of macro 'cs'
26 | namespace cs {
| ^~
/usr/local/include/cs.h:72:3: note: previous declaration 'typedef struct cs_di_sparse cs_di'
72 | } cs_di ;
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:18:6: error: multiple definition of 'enum LogLevel'
18 | enum LogLevel {ERROR, WARNING, INFO, DEBUG, DEBUG1, DEBUG2, DEBUG3, DEBUG4};
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/substitution_matrix-inl.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/log.h:31:6: note: previous definition here
31 | enum LogLevel { ERROR, WARNING, INFO, DEBUG, DEBUG1, DEBUG2, DEBUG3, DEBUG4 };
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:20:7: error: redefinition of 'class Log'
20 | class Log
| ^~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/substitution_matrix-inl.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/log.h:33:7: note: previous definition of 'class Log'
33 | class Log {
| ^~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:38:8: error: redefinition of 'Log::Log()'
38 | inline Log::Log()
| ^~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/substitution_matrix-inl.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/log.h:35:3: note: 'Log::Log()' previously defined here
35 | Log() {}
| ^~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:41:28: error: no declaration matches 'std::ostringstream& Log::Get(LogLevel)'
41 | inline std::ostringstream& Log::Get(LogLevel level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/log.h:41:28: note: no functions named 'std::ostringstream& Log::Get(LogLevel)'
In file included from /Users/mac/lab/guo/hh-suite/src/cs/substitution_matrix-inl.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/log.h:33:7: note: 'class Log' defined here
33 | class Log {
| ^~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h: In static member function 'static LogLevel Log::from_string(const string&)':
/Users/mac/lab/guo/hh-suite/src/log.h:86:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
86 | Log().Get(WARNING) << "Unknown logging level '" << level << "'. Using INFO level as default.";
| ^~~
| get
/Users/mac/lab/guo/hh-suite/src/log.h: In static member function 'static LogLevel Log::from_int(int)':
/Users/mac/lab/guo/hh-suite/src/log.h:107:10: error: 'class Log' has no member named 'Get'; did you mean 'get'?
107 | Log().Get(WARNING) << "Unknown logging level '" << level
| ^~~
| get
In file included from /Users/mac/lab/guo/hh-suite/src/util.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:18,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/util-inl.h: At global scope:
/Users/mac/lab/guo/hh-suite/src/util-inl.h:37:12: error: redefinition of 'int iround(double)'
37 | inline int iround(double x) {
| ^~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/substitution_matrix-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/utils.h:91:12: note: 'int iround(double)' previously defined here
91 | inline int iround(double x) {
| ^~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/util.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:18,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/util-inl.h:108:14: error: redefinition of 'float fast_log2(float)'
108 | inline float fast_log2(float x) {
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/substitution_matrix-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/utils.h:110:14: note: 'float fast_log2(float)' previously defined here
110 | inline float fast_log2(float x) {
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/util.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:18,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/util-inl.h:331:12: error: redefinition of 'int strtoi(const char*&)'
331 | inline int strtoi(const char*& ptr) {
| ^~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/sequence-inl.h:26,
from /Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/io.h:61:12: note: 'int strtoi(const char*&)' previously defined here
61 | inline int strtoi(const char*& ptr) {
| ^~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/util.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:18,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/util-inl.h:378:12: error: redefinition of 'int chomp(char*)'
378 | inline int chomp(char str[]) {
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/sequence-inl.h:26,
from /Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/io.h:39:12: note: 'int chomp(char*)' previously defined here
39 | inline int chomp(char* str) {
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/util.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:18,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/util-inl.h:390:14: error: redefinition of 'char* fgetline(char*, int, FILE*)'
390 | inline char* fgetline(char str[], const int maxlen, FILE* file) {
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/sequence-inl.h:26,
from /Users/mac/lab/guo/hh-suite/src/cs/alignment-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:25,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/io.h:51:14: note: 'char* fgetline(char*, int, FILE*)' previously defined here
51 | inline char* fgetline(char* str, int maxlen, FILE* file) {
| ^~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:99:11: error: 'namespace Pseudocounts { }' redeclared as different kind of entity
99 | namespace Pseudocounts {
| ^~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/pseudocounts-inl.h:22,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:126:7: note: previous declaration 'template<class Abc> class Pseudocounts'
126 | class Pseudocounts {
| ^~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:100:6: error: 'Admix' referred to as enum
100 | enum Admix {
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/pseudocounts-inl.h:22,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:37:8: note: 'Admix' has a previous declaration here
37 | struct Admix {
| ^~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:108:13: error: cannot declare parameter 'm' to be of abstract type 'Admix'
108 | Admix m = ConstantAdmix,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/cs/pseudocounts-inl.h:22,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:37:8: note: because the following virtual functions are pure within 'Admix':
37 | struct Admix {
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:43:20: note: 'virtual double Admix::operator()(double) const'
43 | virtual double operator() (double neff) const = 0;
| ^~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:45:20: note: 'virtual double Admix::GetTargetNeffParam() const'
45 | virtual double GetTargetNeffParam() const = 0;
| ^~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:47:18: note: 'virtual void Admix::SetTargetNeffParam(double)'
47 | virtual void SetTargetNeffParam(double p) = 0;
| ^~~~~~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:115:7: error: 'Admix' in 'cs_di' {aka 'struct cs_di_sparse'} does not name a type
115 | cs::Admix* CreateAdmix() {
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:131:9: error: cannot declare field 'Params::admix' to be of abstract type 'Admix'
131 | Admix admix; // admixture mode
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:200:3: error: invalid use of template-name 'Pseudocounts' without an argument list
200 | Pseudocounts::Params pc_hhm_context_engine; // Pseudocounts parameters for query hhm if context given
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:200:3: note: class template argument deduction is only available with '-std=c++17' or '-std=gnu++17'
In file included from /Users/mac/lab/guo/hh-suite/src/cs/pseudocounts-inl.h:22,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:126:7: note: 'template<class Abc> class Pseudocounts' declared here
126 | class Pseudocounts {
| ^~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:201:3: error: invalid use of template-name 'Pseudocounts' without an argument list
201 | Pseudocounts::Params pc_prefilter_context_engine; // Pseudocounts parameters for prefiltering if context given
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhdecl.h:201:3: note: class template argument deduction is only available with '-std=c++17' or '-std=gnu++17'
In file included from /Users/mac/lab/guo/hh-suite/src/cs/pseudocounts-inl.h:22,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:24,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/pseudocounts.h:126:7: note: 'template<class Abc> class Pseudocounts' declared here
126 | class Pseudocounts {
| ^~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/list.h: In constructor 'List<Typ>::List()':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/list.h:241:5: note: in expansion of macro 'HH_LOG'
241 | HH_LOG(ERROR) << "Could not create new element" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/list.h:246:5: note: in expansion of macro 'HH_LOG'
246 | HH_LOG(ERROR) << "Could not create new element" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/list.h: In constructor 'List<Typ>::List(Typ)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/list.h:263:5: note: in expansion of macro 'HH_LOG'
263 | HH_LOG(ERROR) << "Could not create new element" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/list.h:268:5: note: in expansion of macro 'HH_LOG'
268 | HH_LOG(ERROR) << "Could not create new element" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/list.h:273:5: note: in expansion of macro 'HH_LOG'
273 | HH_LOG(ERROR) << "Could not create new element" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/list.h: In member function 'Typ* List<Typ>::Push(Typ)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/list.h:347:5: note: in expansion of macro 'HH_LOG'
347 | HH_LOG(ERROR) << "Could not create new element" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/list.h: In member function 'Typ* List<Typ>::Enqueue(Typ)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/list.h:384:5: note: in expansion of macro 'HH_LOG'
384 | HH_LOG(ERROR) << "Could not create new element" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/list.h: In member function 'void List<Typ>::Insert(Typ)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/list.h:497:5: note: in expansion of macro 'HH_LOG'
497 | HH_LOG(ERROR) << "Could not create new element!" << std::endl;
| ^~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhhmm.h:10,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:48,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhdatabase.h: At global scope:
/Users/mac/lab/guo/hh-suite/src/hhdatabase.h:13:7: error: template argument required for 'class Alignment'
13 | class Alignment;
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdatabase.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhhmm.h:10,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:48,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhalignment.h:30:7: error: template argument required for 'class Alignment'
30 | class Alignment
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhhmm.h:10,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:48,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhdatabase.h:86:34: error: 'Alignment' is not a type
86 | const float Sim[20][20], Alignment& tali) {};
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhdatabase.h:104:34: error: 'Alignment' is not a type
104 | const float Sim[20][20], Alignment& tali);
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhdatabase.h:122:34: error: 'Alignment' is not a type
122 | const float Sim[20][20], Alignment& tali);
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:48,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhhmm.h:84:43: error: 'cs_di::Pseudocounts' has not been declared
84 | void AddContextSpecificPseudocounts(cs::Pseudocounts<cs::AA>* pc,
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhhmm.h:84:55: error: expected ',' or '...' before '<' token
84 | void AddContextSpecificPseudocounts(cs::Pseudocounts<cs::AA>* pc,
| ^
/Users/mac/lab/guo/hh-suite/src/hhhmm.h:88:29: error: 'cs_di::CountProfile' has not been declared
88 | void fillCountProfile(cs::CountProfile<cs::AA> *csProfile);
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhhmm.h:88:41: error: expected ',' or '...' before '<' token
88 | void fillCountProfile(cs::CountProfile<cs::AA> *csProfile);
| ^
/Users/mac/lab/guo/hh-suite/src/hhhmm.h:176:16: error: template argument required for 'class Alignment'
176 | friend class Alignment;
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhhmm.h:176:3: error: friend declaration does not name a class or function
176 | friend class Alignment;
| ^~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhhmm.h: In member function 'int HMM::Warning(FILE*, char*, char*)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhhmm.h:163:5: note: in expansion of macro 'HH_LOG'
163 | HH_LOG(WARNING) << "Warning in " << __FILE__ << ":" << __LINE__
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhhmm.h:165:5: note: in expansion of macro 'HH_LOG'
165 | HH_LOG(WARNING) << "\tcould not read line\n\'" << line
| ^~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:56,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhfunc.h: At global scope:
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:17:101: error: 'Alignment' is not a type
17 | void ReadQueryFile(Parameters& par, FILE* inf, char& input_format, char use_global_weights, HMM* q, Alignment* qali, char infile[],
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:56,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:20:104: error: 'Alignment' is not a type
20 | void ReadQueryFile(Parameters& par, char* infile, char& input_format, char use_global_weights, HMM* q, Alignment* qali,
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:24:71: error: 'cs_di::Pseudocounts' has not been declared
24 | void PrepareQueryHMM(Parameters& par, char& input_format, HMM* q, cs::Pseudocounts<cs::AA>* pc_hhm_context_engine, cs::Admix* pc_hhm_context_mode,
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:24:83: error: expected ',' or '...' before '<' token
24 | void PrepareQueryHMM(Parameters& par, char& input_format, HMM* q, cs::Pseudocounts<cs::AA>* pc_hhm_context_engine, cs::Admix* pc_hhm_context_mode,
| ^
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:34:9: error: 'cs_di::ContextLibrary' has not been declared
34 | cs::ContextLibrary<cs::AA>*& context_lib, cs::Crf<cs::AA>*& crf,
| ^~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:34:23: error: expected ',' or '...' before '<' token
34 | cs::ContextLibrary<cs::AA>*& context_lib, cs::Crf<cs::AA>*& crf,
| ^
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:38:6: error: variable or field 'DeletePseudocountsEngine' declared void
38 | void DeletePseudocountsEngine(
| ^~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:39:9: error: 'ContextLibrary' is not a member of 'cs_di' {aka 'cs_di_sparse'}
39 | cs::ContextLibrary<cs::AA>* context_lib, cs::Crf<cs::AA>* crf,
| ^~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:39:28: error: 'AA' is not a member of 'cs_di' {aka 'cs_di_sparse'}
39 | cs::ContextLibrary<cs::AA>* context_lib, cs::Crf<cs::AA>* crf,
| ^~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:39:33: error: 'context_lib' was not declared in this scope
39 | cs::ContextLibrary<cs::AA>* context_lib, cs::Crf<cs::AA>* crf,
| ^~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:39:50: error: 'Crf' is not a member of 'cs_di' {aka 'cs_di_sparse'}
39 | cs::ContextLibrary<cs::AA>* context_lib, cs::Crf<cs::AA>* crf,
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:39:58: error: 'AA' is not a member of 'cs_di' {aka 'cs_di_sparse'}
39 | cs::ContextLibrary<cs::AA>* context_lib, cs::Crf<cs::AA>* crf,
| ^~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:39:63: error: 'crf' was not declared in this scope; did you mean 'Crf'?
39 | cs::ContextLibrary<cs::AA>* context_lib, cs::Crf<cs::AA>* crf,
| ^~~
| Crf
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:40:9: error: 'Pseudocounts' is not a member of 'cs_di' {aka 'cs_di_sparse'}
40 | cs::Pseudocounts<cs::AA>* pc_hhm_context_engine, cs::Admix* pc_hhm_context_mode,
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:40:26: error: 'AA' is not a member of 'cs_di' {aka 'cs_di_sparse'}
40 | cs::Pseudocounts<cs::AA>* pc_hhm_context_engine, cs::Admix* pc_hhm_context_mode,
| ^~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:40:31: error: 'pc_hhm_context_engine' was not declared in this scope
40 | cs::Pseudocounts<cs::AA>* pc_hhm_context_engine, cs::Admix* pc_hhm_context_mode,
| ^~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:40:58: error: 'Admix' is not a member of 'cs_di' {aka 'cs_di_sparse'}
40 | cs::Pseudocounts<cs::AA>* pc_hhm_context_engine, cs::Admix* pc_hhm_context_mode,
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:40:65: error: 'pc_hhm_context_mode' was not declared in this scope
40 | cs::Pseudocounts<cs::AA>* pc_hhm_context_engine, cs::Admix* pc_hhm_context_mode,
| ^~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:41:9: error: 'Pseudocounts' is not a member of 'cs_di' {aka 'cs_di_sparse'}
41 | cs::Pseudocounts<cs::AA>* pc_prefilter_context_engine, cs::Admix* pc_prefilter_context_mode);
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:41:26: error: 'AA' is not a member of 'cs_di' {aka 'cs_di_sparse'}
41 | cs::Pseudocounts<cs::AA>* pc_prefilter_context_engine, cs::Admix* pc_prefilter_context_mode);
| ^~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:41:31: error: 'pc_prefilter_context_engine' was not declared in this scope
41 | cs::Pseudocounts<cs::AA>* pc_prefilter_context_engine, cs::Admix* pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:41:64: error: 'Admix' is not a member of 'cs_di' {aka 'cs_di_sparse'}
41 | cs::Pseudocounts<cs::AA>* pc_prefilter_context_engine, cs::Admix* pc_prefilter_context_mode);
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhfunc.h:41:71: error: 'pc_prefilter_context_mode' was not declared in this scope
41 | cs::Pseudocounts<cs::AA>* pc_prefilter_context_engine, cs::Admix* pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.h:60,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhprefilter.h:88:6: error: 'ContextLibrary' in 'cs_di' {aka 'struct cs_di_sparse'} does not name a template type
88 | cs::ContextLibrary<cs::AA> *cs_lib;
| ^~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhblits.h:129:6: error: 'ContextLibrary' in 'cs_di' {aka 'struct cs_di_sparse'} does not name a template type
129 | cs::ContextLibrary<cs::AA>* context_lib;
| ^~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.h:130:6: error: 'Crf' in 'cs_di' {aka 'struct cs_di_sparse'} does not name a template type
130 | cs::Crf<cs::AA>* crf;
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.h:131:6: error: 'Pseudocounts' in 'cs_di' {aka 'struct cs_di_sparse'} does not name a template type
131 | cs::Pseudocounts<cs::AA>* pc_hhm_context_engine;
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.h:132:6: error: 'Admix' in 'cs_di' {aka 'struct cs_di_sparse'} does not name a type
132 | cs::Admix* pc_hhm_context_mode;
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.h:133:6: error: 'Pseudocounts' in 'cs_di' {aka 'struct cs_di_sparse'} does not name a template type
133 | cs::Pseudocounts<cs::AA>* pc_prefilter_context_engine;
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.h:134:6: error: 'Admix' in 'cs_di' {aka 'struct cs_di_sparse'} does not name a type
134 | cs::Admix* pc_prefilter_context_mode;
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.h:145:2: error: invalid use of template-name 'Alignment' without an argument list
145 | Alignment* Qali;
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.h:145:2: note: class template argument deduction is only available with '-std=c++17' or '-std=gnu++17'
In file included from /Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/alignment.h:35:7: note: 'template<class Abc> class Alignment' declared here
35 | class Alignment;
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhblits.h:147:2: error: invalid use of template-name 'Alignment' without an argument list
147 | Alignment* Qali_allseqs;
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.h:147:2: note: class template argument deduction is only available with '-std=c++17' or '-std=gnu++17'
In file included from /Users/mac/lab/guo/hh-suite/src/cs/count_profile.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/count_profile-inl.h:23,
from /Users/mac/lab/guo/hh-suite/src/cs/context_profile.h:24,
from /Users/mac/lab/guo/hh-suite/src/cs/context_library.h:23,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:38,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/cs/alignment.h:35:7: note: 'template<class Abc> class Alignment' declared here
35 | class Alignment;
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhblits.h:153:26: error: template argument 2 is invalid
153 | std::map<int, Alignment*> alis;
| ^
/Users/mac/lab/guo/hh-suite/src/hhblits.h:153:26: error: template argument 4 is invalid
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In constructor 'HHblits::HHblits(Parameters&, std::vector<HHblitsDatabase*>&)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:14:5: error: 'context_lib' was not declared in this scope
14 | context_lib = NULL;
| ^~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:15:5: error: 'crf' was not declared in this scope; did you mean 'Crf'?
15 | crf = NULL;
| ^~~
| Crf
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:16:5: error: 'pc_hhm_context_engine' was not declared in this scope
16 | pc_hhm_context_engine = NULL;
| ^~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:17:5: error: 'pc_hhm_context_mode' was not declared in this scope
17 | pc_hhm_context_mode = NULL;
| ^~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:18:5: error: 'pc_prefilter_context_engine' was not declared in this scope
18 | pc_prefilter_context_engine = NULL;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:19:5: error: 'pc_prefilter_context_mode' was not declared in this scope
19 | pc_prefilter_context_mode = NULL;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:21:5: error: 'Qali' was not declared in this scope
21 | Qali = NULL;
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:22:5: error: 'Qali_allseqs' was not declared in this scope
22 | Qali_allseqs = NULL;
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In destructor 'virtual HHblits::~HHblits()':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:58:30: error: 'context_lib' was not declared in this scope
58 | DeletePseudocountsEngine(context_lib, crf, pc_hhm_context_engine, pc_hhm_context_mode, pc_prefilter_context_engine, pc_prefilter_context_mode);
| ^~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:58:43: error: 'crf' was not declared in this scope; did you mean 'Crf'?
58 | DeletePseudocountsEngine(context_lib, crf, pc_hhm_context_engine, pc_hhm_context_mode, pc_prefilter_context_engine, pc_prefilter_context_mode);
| ^~~
| Crf
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:58:48: error: 'pc_hhm_context_engine' was not declared in this scope
58 | DeletePseudocountsEngine(context_lib, crf, pc_hhm_context_engine, pc_hhm_context_mode, pc_prefilter_context_engine, pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:58:71: error: 'pc_hhm_context_mode' was not declared in this scope
58 | DeletePseudocountsEngine(context_lib, crf, pc_hhm_context_engine, pc_hhm_context_mode, pc_prefilter_context_engine, pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:58:92: error: 'pc_prefilter_context_engine' was not declared in this scope
58 | DeletePseudocountsEngine(context_lib, crf, pc_hhm_context_engine, pc_hhm_context_mode, pc_prefilter_context_engine, pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:58:121: error: 'pc_prefilter_context_mode' was not declared in this scope
58 | DeletePseudocountsEngine(context_lib, crf, pc_hhm_context_engine, pc_hhm_context_mode, pc_prefilter_context_engine, pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:58:5: error: 'DeletePseudocountsEngine' was not declared in this scope; did you mean 'InitializePseudocountsEngine'?
58 | DeletePseudocountsEngine(context_lib, crf, pc_hhm_context_engine, pc_hhm_context_mode, pc_prefilter_context_engine, pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~~~~
| InitializePseudocountsEngine
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In static member function 'static void HHblits::ProcessAllArguments(Parameters&)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:95:9: note: in expansion of macro 'HH_LOG'
95 | HH_LOG(ERROR) << "Input file is missing! (see -i)" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:100:9: note: in expansion of macro 'HH_LOG'
100 | HH_LOG(ERROR) << "Database is missing! (see -d)" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:105:9: note: in expansion of macro 'HH_LOG'
105 | HH_LOG(WARNING)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:116:9: note: in expansion of macro 'HH_LOG'
116 | HH_LOG(WARNING) << "Number of iterations (" << par.num_rounds << ") too large => Set to 8 iterations\n";
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:125:13: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
125 | if (par.pc_hhm_context_engine.pca < 0.001)
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:126:13: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
126 | par.pc_hhm_context_engine.pca = 0.001; // to avoid log(0)
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:127:13: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
127 | if (par.pc_prefilter_context_engine.pca < 0.001)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:128:13: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
128 | par.pc_prefilter_context_engine.pca = 0.001; // to avoid log(0)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:134:9: note: in expansion of macro 'HH_LOG'
134 | HH_LOG(WARNING) << "Setting -maxmem to its minimum allowed value of 1.0" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::Reset()':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:156:9: error: 'Qali' was not declared in this scope
156 | if (Qali) {
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:157:16: error: type '<type error>' argument given to 'delete', expected pointer
157 | delete Qali;
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:161:9: error: 'Qali_allseqs' was not declared in this scope
161 | if (Qali_allseqs) {
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:162:16: error: type '<type error>' argument given to 'delete', expected pointer
162 | delete Qali_allseqs;
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:171:29: error: template argument 2 is invalid
171 | std::map<int, Alignment*>::iterator it;
| ^
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:171:29: error: template argument 4 is invalid
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:171:41: error: qualified-id in declaration before 'it'
171 | std::map<int, Alignment*>::iterator it;
| ^~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:172:10: error: 'it' was not declared in this scope; did you mean 'Hit'?
172 | for (it = alis.begin(); it != alis.end(); it++) {
| ^~
| Hit
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:172:20: error: request for member 'begin' in '((HHblits*)this)->HHblits::alis', which is of non-class type 'int'
172 | for (it = alis.begin(); it != alis.end(); it++) {
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:172:40: error: request for member 'end' in '((HHblits*)this)->HHblits::alis', which is of non-class type 'int'
172 | for (it = alis.begin(); it != alis.end(); it++) {
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:175:10: error: request for member 'clear' in '((HHblits*)this)->HHblits::alis', which is of non-class type 'int'
175 | alis.clear();
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In static member function 'static void HHblits::help(Parameters&, char)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:333:124: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
333 | printf(" -pc_hhm_contxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=%-i) \n", par.pc_hhm_context_engine.admix);
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:339:124: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
339 | printf(" -pc_hhm_contxt_a [0,1] overall pseudocount admixture (def=%-.1f) \n", par.pc_hhm_context_engine.pca);
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:340:124: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
340 | printf(" -pc_hhm_contxt_b [1,inf[ Neff threshold value for mode 2 (def=%-.1f) \n", par.pc_hhm_context_engine.pcb);
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:341:124: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
341 | printf(" -pc_hhm_contxt_c [0,3] extinction exponent c for mode 2 (def=%-.1f) \n", par.pc_hhm_context_engine.pcc);
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:356:130: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
356 | printf(" -pc_prefilter_contxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=%-i) \n", par.pc_prefilter_context_engine.admix);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:362:130: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
362 | printf(" -pc_prefilter_contxt_a [0,1] overall pseudocount admixture (def=%-.1f) \n", par.pc_prefilter_context_engine.pca);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:363:130: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
363 | printf(" -pc_prefilter_contxt_b [1,inf[ Neff threshold value for mode 2 (def=%-.1f) \n", par.pc_prefilter_context_engine.pcb);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:364:130: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
364 | printf(" -pc_prefilter_contxt_c [0,3] extinction exponent c for mode 2 (def=%-.1f) \n", par.pc_prefilter_context_engine.pcc);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In static member function 'static void HHblits::ProcessArguments(Parameters&)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:420:9: note: in expansion of macro 'HH_LOG'
420 | HH_LOG(DEBUG1) << i << " " << argv[i] << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:424:17: note: in expansion of macro 'HH_LOG'
424 | HH_LOG(ERROR) << "No query file following -i" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:431:17: note: in expansion of macro 'HH_LOG'
431 | HH_LOG(ERROR) << "No database basename following -d" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:436:21: note: in expansion of macro 'HH_LOG'
436 | HH_LOG(ERROR) << "Ambiguous database basename. Choose either a A3M or CA3M database." << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:445:17: note: in expansion of macro 'HH_LOG'
445 | HH_LOG(ERROR) << "No lib following -contxt" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:452:17: note: in expansion of macro 'HH_LOG'
452 | HH_LOG(ERROR) << "No lib following -cslib" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:459:17: note: in expansion of macro 'HH_LOG'
459 | HH_LOG(ERROR) << "No output file following -o" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:468:17: note: in expansion of macro 'HH_LOG'
468 | HH_LOG(ERROR) << "No output file following -omat" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:475:17: note: in expansion of macro 'HH_LOG'
475 | HH_LOG(ERROR) << "No output file following -oa3m" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:484:17: note: in expansion of macro 'HH_LOG'
484 | HH_LOG(ERROR) << "No output file following -ohhm" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:491:17: note: in expansion of macro 'HH_LOG'
491 | HH_LOG(ERROR) << "No output file following -opsi" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:498:17: note: in expansion of macro 'HH_LOG'
498 | HH_LOG(ERROR) << "No file basename following -oalis" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:508:17: note: in expansion of macro 'HH_LOG'
508 | HH_LOG(ERROR) << "No output file following -o" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:517:17: note: in expansion of macro 'HH_LOG'
517 | HH_LOG(ERROR) << "No output file following -o" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:526:17: note: in expansion of macro 'HH_LOG'
526 | HH_LOG(ERROR) << "No output file following -o" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:534:17: note: in expansion of macro 'HH_LOG'
534 | HH_LOG(ERROR) << "No file following -scores" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:543:17: note: in expansion of macro 'HH_LOG'
543 | HH_LOG(ERROR) << "No file following -blasttab" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:552:17: note: in expansion of macro 'HH_LOG'
552 | HH_LOG(ERROR) << "No file following -atab" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:584:13: note: in expansion of macro 'HH_LOG'
584 | HH_LOG(WARNING) << "Ignoring unknown option " << argv[i] << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:594:13: note: in expansion of macro 'HH_LOG'
594 | HH_LOG(WARNING) << "Ignoring unknown argument: -M " << argv[i] << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:648:17: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
648 | par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) atoi(argv[++i]);
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:648:48: error: 'template<class Abc> class Pseudocounts' used without template arguments
648 | par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) atoi(argv[++i]);
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:650:17: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
650 | par.pc_hhm_context_engine.pca = atof(argv[++i]);
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:652:17: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
652 | par.pc_hhm_context_engine.pcb = atof(argv[++i]);
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:654:17: error: 'class Parameters' has no member named 'pc_hhm_context_engine'; did you mean 'pc_hhm_nocontext_mode'?
654 | par.pc_hhm_context_engine.pcc = atof(argv[++i]);
| ^~~~~~~~~~~~~~~~~~~~~
| pc_hhm_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:657:17: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
657 | par.pc_prefilter_context_engine.admix = (Pseudocounts::Admix) atoi(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:657:54: error: 'template<class Abc> class Pseudocounts' used without template arguments
657 | par.pc_prefilter_context_engine.admix = (Pseudocounts::Admix) atoi(
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:660:17: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
660 | par.pc_prefilter_context_engine.pca = atof(argv[++i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:662:17: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
662 | par.pc_prefilter_context_engine.pcb = atof(argv[++i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:664:17: error: 'class Parameters' has no member named 'pc_prefilter_context_engine'; did you mean 'pc_prefilter_nocontext_mode'?
664 | par.pc_prefilter_context_engine.pcc = atof(argv[++i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| pc_prefilter_nocontext_mode
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:799:17: note: in expansion of macro 'HH_LOG'
799 | HH_LOG(ERROR) << "No state following -interim_filter" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:808:21: note: in expansion of macro 'HH_LOG'
808 | HH_LOG(ERROR) << "No state out of NONE|FULL following -interim_filter" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:814:13: note: in expansion of macro 'HH_LOG'
814 | HH_LOG(WARNING) << "Ignoring unknown option " << argv[i] << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:817:9: note: in expansion of macro 'HH_LOG'
817 | HH_LOG(DEBUG1) << i << " " << argv[i] << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::mergeHitsToQuery(HitList&, Hash<Hit>*, Hash<Hit>*, int&, int&, int)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:826:54: error: 'Qali' was not declared in this scope
826 | int cov_tot = std::max(std::min((int) (COV_ABS / Qali->L * 100 + 0.5), 70), par.coverage);
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:856:19: error: missing template arguments before 'Tali'
856 | Alignment Tali(par.maxseq, par.maxres);
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:857:56: error: 'Tali' was not declared in this scope
857 | hit_cur.entry->getTemplateA3M(par, pb, S, Sim, Tali);
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:860:13: error: 'Qali_allseqs' was not declared in this scope
860 | Qali_allseqs->MergeMasterSlave(hit_cur, Tali, hit_cur.name, par.maxcol);
| ^~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:883:5: note: in expansion of macro 'HH_LOG'
883 | HH_LOG(DEBUG) << "Filter new alignment with cov " << cov_tot
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::add_hits_to_hitlist(std::vector<Hit>&, HitList&)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:896:5: note: in expansion of macro 'HH_LOG'
896 | HH_LOG(DEBUG) << "Sorting hit list ...\n";
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::RescoreWithViterbiKeepAlignment(HMMSimd&, Hash<Hit>*)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:959:5: note: in expansion of macro 'HH_LOG'
959 | HH_LOG(DEBUG) << "Sorting hit list ..." << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::perform_realign(HMMSimd&, char, std::vector<HHEntry*>&, int)':
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1028:5: note: in expansion of macro 'HH_LOG'
1028 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1054:11: note: in expansion of macro 'HH_LOG'
1054 | HH_LOG(DEBUG) << "Deleting alignment of " << hit_cur.name
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'virtual void HHblits::run(FILE*, char*)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1074:5: error: 'Qali' was not declared in this scope
1074 | Qali = new Alignment(par.maxseq, par.maxres);
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1074:16: error: expected type-specifier before 'Alignment'
1074 | Qali = new Alignment(par.maxseq, par.maxres);
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1075:5: error: 'Qali_allseqs' was not declared in this scope
1075 | Qali_allseqs = new Alignment(par.maxseq, par.maxres);
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1075:24: error: expected type-specifier before 'Alignment'
1075 | Qali_allseqs = new Alignment(par.maxseq, par.maxres);
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1119:9: note: in expansion of macro 'HH_LOG'
1119 | HH_LOG(INFO) << "Iteration " << round << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1122:13: note: in expansion of macro 'HH_LOG'
1122 | HH_LOG(INFO) << "Set premerge to 0! (premerge: " << par.premerge << " iteration: " <<round << " hits.Size: " << previous_hits->Size() << ")\n";
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1132:47: error: 'pc_hhm_context_engine' was not declared in this scope
1132 | PrepareQueryHMM(par, input_format, q, pc_hhm_context_engine,
| ^~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1133:25: error: 'pc_hhm_context_mode' was not declared in this scope
1133 | pc_hhm_context_mode, pb, R);
| ^~~~~~~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1143:13: note: in expansion of macro 'HH_LOG'
1143 | HH_LOG(INFO) << "Prefiltering database" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1159:55: error: 'pc_prefilter_context_engine' was not declared in this scope
1159 | q_tmp->AddContextSpecificPseudocounts(pc_prefilter_context_engine,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1160:55: error: 'pc_prefilter_context_mode' was not declared in this scope
1160 | pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1189:11: note: in expansion of macro 'HH_LOG'
1189 | HH_LOG(WARNING)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1202:13: note: in expansion of macro 'HH_LOG'
1202 | HH_LOG(INFO) << "No HMMs pass prefilter => Stop searching!" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1208:13: note: in expansion of macro 'HH_LOG'
1208 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1210:13: note: in expansion of macro 'HH_LOG'
1210 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1213:9: note: in expansion of macro 'HH_LOG'
1213 | HH_LOG(INFO) << "Scoring " << new_entries.size() << " HMMs using HMM-HMM Viterbi alignment" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1237:17: note: in expansion of macro 'HH_LOG'
1237 | HH_LOG(INFO) << "No new hits found in iteration " << round
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1242:17: note: in expansion of macro 'HH_LOG'
1242 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1256:17: note: in expansion of macro 'HH_LOG'
1256 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1282:26: error: missing template arguments before '*' token
1282 | Alignment* tmp = new Alignment(par.maxseq, par.maxres);
| ^
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1282:28: error: 'tmp' was not declared in this scope; did you mean 'tm'?
1282 | Alignment* tmp = new Alignment(par.maxseq, par.maxres);
| ^~~
| tm
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1282:38: error: expected type-specifier before 'Alignment'
1282 | Alignment* tmp = new Alignment(par.maxseq, par.maxres);
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1289:21: error: invalid types 'int[int]' for array subscript
1289 | alis[round] = tmp;
| ^
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1319:9: note: in expansion of macro 'HH_LOG'
1319 | HH_LOG(INFO) << seqs_found << " sequences belonging to "
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1326:13: note: in expansion of macro 'HH_LOG'
1326 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1332:13: note: in expansion of macro 'HH_LOG'
1332 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1339:13: note: in expansion of macro 'HH_LOG'
1339 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1399:9: note: in expansion of macro 'HH_LOG'
1399 | HH_LOG(WARNING)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::run(ffindex_entry_t*, char*, ffindex_index_t*, char*, ffindex_index_t*, char*)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1424:5: error: 'Qali' was not declared in this scope
1424 | Qali = new Alignment(par.maxseq, par.maxres);
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1424:16: error: expected type-specifier before 'Alignment'
1424 | Qali = new Alignment(par.maxseq, par.maxres);
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1425:5: error: 'Qali_allseqs' was not declared in this scope
1425 | Qali_allseqs = new Alignment(par.maxseq, par.maxres);
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1425:24: error: expected type-specifier before 'Alignment'
1425 | Qali_allseqs = new Alignment(par.maxseq, par.maxres);
| ^~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1511:9: note: in expansion of macro 'HH_LOG'
1511 | HH_LOG(INFO) << "Iteration " << round << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1515:13: note: in expansion of macro 'HH_LOG'
1515 | HH_LOG(INFO) << "Set premerge to 0! (premerge: " << par.premerge << " iteration: " <<round << " hits.Size: " << previous_hits->Size() << ")\n";
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1525:47: error: 'pc_hhm_context_engine' was not declared in this scope
1525 | PrepareQueryHMM(par, input_format, q, pc_hhm_context_engine,
| ^~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1526:25: error: 'pc_hhm_context_mode' was not declared in this scope
1526 | pc_hhm_context_mode, pb, R);
| ^~~~~~~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1536:13: note: in expansion of macro 'HH_LOG'
1536 | HH_LOG(INFO) << "Prefiltering database" << std::endl;
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1552:55: error: 'pc_prefilter_context_engine' was not declared in this scope
1552 | q_tmp->AddContextSpecificPseudocounts(pc_prefilter_context_engine,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1553:55: error: 'pc_prefilter_context_mode' was not declared in this scope
1553 | pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1582:13: note: in expansion of macro 'HH_LOG'
1582 | HH_LOG(WARNING)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1595:13: note: in expansion of macro 'HH_LOG'
1595 | HH_LOG(INFO) << "No HMMs pass prefilter => Stop searching!"
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1601:9: note: in expansion of macro 'HH_LOG'
1601 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1604:9: note: in expansion of macro 'HH_LOG'
1604 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1607:9: note: in expansion of macro 'HH_LOG'
1607 | HH_LOG(INFO) << "Scoring " << new_entries.size()
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1634:17: note: in expansion of macro 'HH_LOG'
1634 | HH_LOG(INFO) << "No new hits found in iteration " << round
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1639:17: note: in expansion of macro 'HH_LOG'
1639 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1653:17: note: in expansion of macro 'HH_LOG'
1653 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1679:26: error: missing template arguments before '*' token
1679 | Alignment* tmp = new Alignment(par.maxseq, par.maxres);
| ^
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1679:28: error: 'tmp' was not declared in this scope; did you mean 'tm'?
1679 | Alignment* tmp = new Alignment(par.maxseq, par.maxres);
| ^~~
| tm
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1679:38: error: expected type-specifier before 'Alignment'
1679 | Alignment* tmp = new Alignment(par.maxseq, par.maxres);
| ^~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1686:21: error: invalid types 'int[int]' for array subscript
1686 | alis[round] = tmp;
| ^
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1716:9: note: in expansion of macro 'HH_LOG'
1716 | HH_LOG(INFO) << seqs_found << " sequences belonging to "
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1723:13: note: in expansion of macro 'HH_LOG'
1723 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1729:13: note: in expansion of macro 'HH_LOG'
1729 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1736:13: note: in expansion of macro 'HH_LOG'
1736 | HH_LOG(INFO)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1797:9: note: in expansion of macro 'HH_LOG'
1797 | HH_LOG(WARNING)
| ^~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::writeAlisFile(char*)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1827:33: error: template argument 2 is invalid
1827 | std::map<int, Alignment*>::iterator it;
| ^
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1827:33: error: template argument 4 is invalid
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1827:45: error: qualified-id in declaration before 'it'
1827 | std::map<int, Alignment*>::iterator it;
| ^~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1828:14: error: 'it' was not declared in this scope; did you mean 'Hit'?
1828 | for (it = alis.begin(); it != alis.end(); it++) {
| ^~
| Hit
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1828:24: error: request for member 'begin' in '((HHblits*)this)->HHblits::alis', which is of non-class type 'int'
1828 | for (it = alis.begin(); it != alis.end(); it++) {
| ^~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1828:44: error: request for member 'end' in '((HHblits*)this)->HHblits::alis', which is of non-class type 'int'
1828 | for (it = alis.begin(); it != alis.end(); it++) {
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::writePsiFile(char*)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1869:13: error: 'Qali_allseqs' was not declared in this scope
1869 | Qali_allseqs->WriteToFile(psiFile, par.append, "psi");
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1871:13: error: 'Qali' was not declared in this scope
1871 | Qali->WriteToFile(psiFile, par.append, "psi");
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::writeA3MFile(char*)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1891:13: error: 'Qali_allseqs' was not declared in this scope
1891 | Qali_allseqs->WriteToFile(A3MFile, par.append, "a3m");
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1893:13: error: 'Qali' was not declared in this scope
1893 | Qali->WriteToFile(A3MFile, par.append, "a3m");
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In static member function 'static void HHblits::writePsiFile(HHblits&, std::stringstream&)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1949:17: error: 'class HHblits' has no member named 'Qali_allseqs'
1949 | hhblits.Qali_allseqs->WriteToFile(out, "psi");
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1951:17: error: 'class HHblits' has no member named 'Qali'
1951 | hhblits.Qali->WriteToFile(out, "psi");
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In static member function 'static void HHblits::writeA3MFile(HHblits&, std::stringstream&)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1966:17: error: 'class HHblits' has no member named 'Qali_allseqs'
1966 | hhblits.Qali_allseqs->WriteToFile(out, "a3m");
| ^~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:1968:17: error: 'class HHblits' has no member named 'Qali'
1968 | hhblits.Qali->WriteToFile(out, "a3m");
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp: In member function 'void HHblits::premerge(Hash<Hit>*, Hash<Hit>*, int&, int&, int)':
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:2039:9: error: 'Qali' was not declared in this scope
2039 | Qali->FrequenciesAndTransitions(q, par.wg, par.mark, par.cons,par.showcons, pb, Sim, NULL,true);
| ^~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:2053:47: error: 'pc_prefilter_context_engine' was not declared in this scope
2053 | q->AddContextSpecificPseudocounts(pc_prefilter_context_engine,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:2054:47: error: 'pc_prefilter_context_mode' was not declared in this scope
2054 | pc_prefilter_context_mode);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /Users/mac/lab/guo/hh-suite/src/hhdecl.h:17,
from /Users/mac/lab/guo/hh-suite/src/hhblits.h:42,
from /Users/mac/lab/guo/hh-suite/src/hhblits.cpp:8:
/Users/mac/lab/guo/hh-suite/src/log.h:116:11: error: 'class Log' has no member named 'Get'; did you mean 'get'?
116 | Log().Get(level)
| ^~~
/Users/mac/lab/guo/hh-suite/src/hhblits.cpp:2064:5: note: in expansion of macro 'HH_LOG'
2064 | HH_LOG(INFO) << "Premerge done\n";
| ^~~~~~
make[2]: *** [src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/HH_OBJECTS.dir/all] Error 2
make: *** [all] Error 2
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