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essaMEM is an algorithm for calculating maximal exact matches using enhanced sparse suffix arrays

License: Other

C++ 86.28% C 13.72%

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essamem's Issues

Fails to compile on linux

(py36) [ksahlin@rackham essaMEM]$ make
g++ -MM mummer.cpp qsufsort.c sparseSA.cpp fasta.cpp > .depend
g++ -O3 -DNDEBUG -Wall -c mummer.cpp
In file included from mummer.cpp:6:
sparseSA.hpp: In member function ‘long int sparseSA::index_size_in_bytes()’:
sparseSA.hpp:110:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(int i = 0; i < descr.size(); i++){
                      ~~^~~~~~~~~~~~~~
mummer.cpp: In function ‘void* query_thread(void*)’:
mummer.cpp:92:10: error: reference to ‘forward’ is ambiguous
       if(forward){
          ^~~~~~~
In file included from /usr/include/c++/8/bits/nested_exception.h:40,
                 from /usr/include/c++/8/exception:144,
                 from /usr/include/c++/8/ios:39,
                 from /usr/include/c++/8/ostream:38,
                 from /usr/include/c++/8/iostream:39,
                 from mummer.cpp:1:
/usr/include/c++/8/bits/move.h:85:5: note: candidates are: ‘template<class _Tp> constexpr _Tp&& std::forward(typename std::remove_reference<_Tp>::type&&)’
     forward(typename std::remove_reference<_Tp>::type&& __t) noexcept
     ^~~~~~~
/usr/include/c++/8/bits/move.h:74:5: note:                 ‘template<class _Tp> constexpr _Tp&& std::forward(typename std::remove_reference<_Tp>::type&)’
     forward(typename std::remove_reference<_Tp>::type& __t) noexcept
     ^~~~~~~
mummer.cpp:29:6: note:                 ‘bool forward’
 bool forward = true;
      ^~~~~~~
mummer.cpp:144:10: error: reference to ‘forward’ is ambiguous
       if(forward){
          ^~~~~~~
In file included from /usr/include/c++/8/bits/nested_exception.h:40,
                 from /usr/include/c++/8/exception:144,
                 from /usr/include/c++/8/ios:39,
                 from /usr/include/c++/8/ostream:38,
                 from /usr/include/c++/8/iostream:39,
                 from mummer.cpp:1:
/usr/include/c++/8/bits/move.h:85:5: note: candidates are: ‘template<class _Tp> constexpr _Tp&& std::forward(typename std::remove_reference<_Tp>::type&&)’
     forward(typename std::remove_reference<_Tp>::type&& __t) noexcept
     ^~~~~~~
/usr/include/c++/8/bits/move.h:74:5: note:                 ‘template<class _Tp> constexpr _Tp&& std::forward(typename std::remove_reference<_Tp>::type&)’
     forward(typename std::remove_reference<_Tp>::type& __t) noexcept
     ^~~~~~~
mummer.cpp:29:6: note:                 ‘bool forward’
 bool forward = true;
      ^~~~~~~
mummer.cpp: In function ‘int main(int, char**)’:
mummer.cpp:290:7: error: reference to ‘forward’ is ambiguous
       forward = false;
       ^~~~~~~
In file included from /usr/include/c++/8/bits/nested_exception.h:40,
                 from /usr/include/c++/8/exception:144,
                 from /usr/include/c++/8/ios:39,
                 from /usr/include/c++/8/ostream:38,
                 from /usr/include/c++/8/iostream:39,
                 from mummer.cpp:1:
/usr/include/c++/8/bits/move.h:85:5: note: candidates are: ‘template<class _Tp> constexpr _Tp&& std::forward(typename std::remove_reference<_Tp>::type&&)’
     forward(typename std::remove_reference<_Tp>::type&& __t) noexcept
     ^~~~~~~
/usr/include/c++/8/bits/move.h:74:5: note:                 ‘template<class _Tp> constexpr _Tp&& std::forward(typename std::remove_reference<_Tp>::type&)’
     forward(typename std::remove_reference<_Tp>::type& __t) noexcept
     ^~~~~~~
mummer.cpp:29:6: note:                 ‘bool forward’
 bool forward = true;
      ^~~~~~~
make: *** [Makefile:10: mummer.o] Error 1

Fails to compile on MacOSX 10.10

(Possibly a Clang vs GCC issue)

Error:

g++ -O3 -DNDEBUG -Wall -c mummer.cpp
mummer.cpp:93:10: error: reference to 'forward' is ambiguous
      if(forward){
         ^
mummer.cpp:28:6: note: candidate found by name lookup is 'forward'
bool forward = true;
     ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/type_traits:1583:1: note: candidate found by name lookup is 'std::__1::forward'
forward(typename std::remove_reference<_Tp>::type& __t) _NOEXCEPT
^
mummer.cpp:93:10: error: unknown type name 'forward'
      if(forward){
         ^
mummer.cpp:93:17: error: expected unqualified-id
      if(forward){
                ^
mummer.cpp:93:17: error: variable declaration in condition must have an initializer
mummer.cpp:145:10: error: reference to 'forward' is ambiguous
      if(forward){
         ^
mummer.cpp:28:6: note: candidate found by name lookup is 'forward'
bool forward = true;
     ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/type_traits:1583:1: note: candidate found by name lookup is 'std::__1::forward'
forward(typename std::remove_reference<_Tp>::type& __t) _NOEXCEPT
^
mummer.cpp:145:10: error: unknown type name 'forward'
      if(forward){
         ^
mummer.cpp:145:17: error: expected unqualified-id
      if(forward){
                ^
mummer.cpp:145:17: error: variable declaration in condition must have an initializer
mummer.cpp:312:7: error: reference to 'forward' is ambiguous
      forward = false;
      ^
mummer.cpp:28:6: note: candidate found by name lookup is 'forward'
bool forward = true;
     ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/type_traits:1583:1: note: candidate found by name lookup is 'std::__1::forward'
forward(typename std::remove_reference<_Tp>::type& __t) _NOEXCEPT
^
9 errors generated.
make: *** [mummer.o] Error 1

Particulars:

Darwin edna 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64 x86_64

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