error: cannot bind non-const lvalue reference of type ‘AFP&’ to an rvalue of type ‘AFP’

[lucajovine]

Hello, when installing FATCAT under Ubuntu 20.94, I get the following:

g++ -O2 -Wall -I./ -c FATCAT.C
g++ -O2 -Wall -I./ -c SAlnOpt.C
g++ -O2 -Wall -I./ -c SigEva.C
SigEva.C: In member function ‘double SIGEVA::calSig(int, int, int, double*)’:
SigEva.C:256:9: warning: variable ‘prob0’ set but not used [-Wunused-but-set-variable]
  double prob0;
         ^~~~~
g++ -O2 -Wall -I./ -c Prot.C
g++ -O2 -Wall -I./ -c AFPchain.C
AFPchain.C:872:1: warning: multi-line comment [-Wcomment]
 //       j1 -|---------------------\
 ^
AFPchain.C: In member function ‘void AFPCHAIN::MergeAfp(int, int*, int*)’:
AFPchain.C:445:35: warning: variable ‘j2’ set but not used [-Wunused-but-set-variable]
  int i, j, k, f1, f2, i1, i2, j1, j2, frag;
                                   ^~
AFPchain.C: In member function ‘void AFPCHAIN::UpdateScore()’:
AFPchain.C:1154:9: warning: variable ‘t’ set but not used [-Wunused-but-set-variable]
  double t, conn, dvar;
         ^
AFPchain.C: In member function ‘void AFPCHAIN::ShowAfpChainText()’:
AFPchain.C:1327:28: warning: variable ‘t’ set but not used [-Wunused-but-set-variable]
  int i, k, a, len, pi, pj, t, mis, gap, prev;
                            ^
AFPchain.C: In member function ‘void AFPCHAIN::ShowAfpChainPs()’:
AFPchain.C:1437:68: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  PsShow *psShow = new PsShow(outfile, "alignment graph from FATCAT"); //refer PsShow.C and PsShow.h
                                                                    ^
AFPchain.C: In member function ‘void AFPCHAIN::ShowAfp(int)’:
AFPchain.C:1463:123: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  PsShow *psShow = new PsShow(outfile, "%!PS-Adobe-3.0 EPSF-3.0\n%%BoundingBox: 0 0 500 500", "alignment graph from FATCAT"); //refer PsShow.C and PsShow.h
                                                                                                                           ^
AFPchain.C:1463:123: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AFPchain.C:1559:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  psShow->prtArrow(arrowpoint, blockNum - 1, ifcodtransform, "downleftarrow");
                                                                            ^
AFPchain.C: In member function ‘void AFPCHAIN::TransPdb(int, int*, int*)’:
AFPchain.C:1727:21: warning: variable ‘rmsd’ set but not used [-Wunused-but-set-variable]
  double r[9], t[3], rmsd;
                     ^~~~
In file included from /usr/include/c++/7/vector:69:0,
                 from basic.h:8,
                 from AFP.h:13,
                 from AFPchain.h:13,
                 from AFPchain.C:12:
/usr/include/c++/7/bits/vector.tcc: In instantiation of ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, _Arg&&) [with _Arg = AFP; _Tp = AFP; _Alloc = std::allocator<AFP>; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >; typename std::_Vector_base<_Tp, _Alloc>::pointer = AFP*]’:
/usr/include/c++/7/bits/vector.tcc:136:19:   required from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = AFP; _Alloc = std::allocator<AFP>; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >; typename std::_Vector_base<_Tp, _Alloc>::pointer = AFP*; std::vector<_Tp, _Alloc>::const_iterator = __gnu_cxx::__normal_iterator<const AFP*, std::vector<AFP> >; typename __gnu_cxx::__alloc_traits<typename std::_Vector_base<_Tp, _Alloc>::_Tp_alloc_type>::const_pointer = const AFP*; std::vector<_Tp, _Alloc>::value_type = AFP]’
AFPchain.C:315:39:   required from here
/usr/include/c++/7/bits/vector.tcc:386:19: error: cannot bind non-const lvalue reference of type ‘AFP&’ to an rvalue of type ‘AFP’
       *__position = std::forward<_Arg>(__arg);
       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from AFPchain.h:13:0,
                 from AFPchain.C:12:
AFP.h:103:8: note:   initializing argument 1 of ‘void AFP::operator=(AFP&)’
   void operator = (AFP &afp)
        ^~~~~~~~
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
                 from /usr/include/c++/7/ios:40,
                 from /usr/include/c++/7/ostream:38,
                 from /usr/include/c++/7/iostream:39,
                 from basic.h:3,
                 from AFP.h:13,
                 from AFPchain.h:13,
                 from AFPchain.C:12:
/usr/include/c++/7/bits/stl_algobase.h: In instantiation of ‘static _BI2 std::__copy_move_backward<true, false, std::random_access_iterator_tag>::__copy_move_b(_BI1, _BI1, _BI2) [with _BI1 = AFP*; _BI2 = AFP*]’:
/usr/include/c++/7/bits/stl_algobase.h:588:58:   required from ‘_BI2 std::__copy_move_backward_a(_BI1, _BI1, _BI2) [with bool _IsMove = true; _BI1 = AFP*; _BI2 = AFP*]’
/usr/include/c++/7/bits/stl_algobase.h:598:5:   required from ‘_BI2 std::__copy_move_backward_a2(_BI1, _BI1, _BI2) [with bool _IsMove = true; _BI1 = AFP*; _BI2 = AFP*]’
/usr/include/c++/7/bits/stl_algobase.h:668:48:   required from ‘_BI2 std::move_backward(_BI1, _BI1, _BI2) [with _BI1 = AFP*; _BI2 = AFP*]’
/usr/include/c++/7/bits/vector.tcc:380:7:   required from ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, _Arg&&) [with _Arg = AFP; _Tp = AFP; _Alloc = std::allocator<AFP>; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >; typename std::_Vector_base<_Tp, _Alloc>::pointer = AFP*]’
/usr/include/c++/7/bits/vector.tcc:136:19:   required from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = AFP; _Alloc = std::allocator<AFP>; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >; typename std::_Vector_base<_Tp, _Alloc>::pointer = AFP*; std::vector<_Tp, _Alloc>::const_iterator = __gnu_cxx::__normal_iterator<const AFP*, std::vector<AFP> >; typename __gnu_cxx::__alloc_traits<typename std::_Vector_base<_Tp, _Alloc>::_Tp_alloc_type>::const_pointer = const AFP*; std::vector<_Tp, _Alloc>::value_type = AFP]’
AFPchain.C:315:39:   required from here
/usr/include/c++/7/bits/stl_algobase.h:548:18: error: cannot bind non-const lvalue reference of type ‘AFP&’ to an rvalue of type ‘std::remove_reference<AFP&>::type {aka AFP}’
      *--__result = std::move(*--__last);
      ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
In file included from AFPchain.h:13:0,
                 from AFPchain.C:12:
AFP.h:103:8: note:   initializing argument 1 of ‘void AFP::operator=(AFP&)’
   void operator = (AFP &afp)
        ^~~~~~~~
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
                 from /usr/include/c++/7/ios:40,
                 from /usr/include/c++/7/ostream:38,
                 from /usr/include/c++/7/iostream:39,
                 from basic.h:3,
                 from AFP.h:13,
                 from AFPchain.h:13,
                 from AFPchain.C:12:
/usr/include/c++/7/bits/stl_algobase.h: In instantiation of ‘static _OI std::__copy_move<true, false, std::random_access_iterator_tag>::__copy_m(_II, _II, _OI) [with _II = AFP*; _OI = AFP*]’:
/usr/include/c++/7/bits/stl_algobase.h:386:44:   required from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = true; _II = AFP*; _OI = AFP*]’
/usr/include/c++/7/bits/stl_algobase.h:422:45:   required from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = true; _II = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >; _OI = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >]’
/usr/include/c++/7/bits/stl_algobase.h:487:39:   required from ‘_OI std::move(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >; _OI = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >]’
/usr/include/c++/7/bits/vector.tcc:171:6:   required from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = AFP; _Alloc = std::allocator<AFP>; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >; typename std::_Vector_base<_Tp, _Alloc>::pointer = AFP*]’
/usr/include/c++/7/bits/stl_vector.h:1210:17:   required from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::const_iterator) [with _Tp = AFP; _Alloc = std::allocator<AFP>; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<AFP*, std::vector<AFP> >; typename std::_Vector_base<_Tp, _Alloc>::pointer = AFP*; std::vector<_Tp, _Alloc>::const_iterator = __gnu_cxx::__normal_iterator<const AFP*, std::vector<AFP> >; typename __gnu_cxx::__alloc_traits<typename std::_Vector_base<_Tp, _Alloc>::_Tp_alloc_type>::const_pointer = const AFP*]’
AFPchain.C:425:43:   required from here
/usr/include/c++/7/bits/stl_algobase.h:343:18: error: cannot bind non-const lvalue reference of type ‘AFP&’ to an rvalue of type ‘std::remove_reference<AFP&>::type {aka AFP}’
        *__result = std::move(*__first);
        ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from AFPchain.h:13:0,
                 from AFPchain.C:12:
AFP.h:103:8: note:   initializing argument 1 of ‘void AFP::operator=(AFP&)’
   void operator = (AFP &afp)
        ^~~~~~~~
make: *** [Makefile:27: AFPchain.o] Error 1

Could you please let me know how to fix this? Thanks!

[davidhbrann]

I received the same error, but was able to install it after using gcc/g++ 4.8.5 instead of 6.2.0 or 9.2.0

[lucajovine]

Thanks for the reply, but where to find a distribution of that gcc/g++ version for 20.04?
Alternatively, I suppose I can simply use the executables within the FATCAT-dist/FATCATMain directory... or?

[krcurtis]

I had success in compiling and checking the example describe in the Install file when specifying which C++ standard to use to the Makefile:
CCOPT = -O2 -Wall --std=c++03
and changing the line about #include <string> to #include <cstring> in basic.h. I'm not entirely sure if those are quite the correct changes to make though.