Gerp++ installation error

Question

[Abdul Rafay Khan]

I am trying to compile gerp++ source code on Ubuntu 18.04.1 LTS but i am getting error using make command.

sudo make
g++ -Wall -W -pedantic -O4 -c MIter.cc
g++ -Wall -W -pedantic -O4 -c Mseq.cc
Mseq.cc: In member function ‘Vec<char> Mseq::getAlignment(Seq::size_type, Seq::size_type) const’:
Mseq.cc:328:16: warning: variable ‘X_end’ set but not used [-Wunused-but-set-variable]
                X_end = X.getEnd(),
                ^~~~~
Mseq.cc:329:16: warning: variable ‘Y_end’ set but not used [-Wunused-but-set-variable]
                Y_end = Y.getEnd();
                ^~~~~
g++ -Wall -W -pedantic -O4 -c Seq.cc
g++ -Wall -W -pedantic -O4 -c etree.cc
g++ -Wall -W -pedantic -O4 -c emodel.cc
g++ -Wall -W -pedantic -O4 -c gerpcol.cc
gerpcol.cc: In function ‘void estimateFreqs(std::vector<std::__cxx11::basic_string<char> >&, double*)’:
gerpcol.cc:154:49: error: no matching function for call to ‘find(std::vector<std::__cxx11::basic_string<char> >::iterator, std::vector<std::__cxx11::basic_string<char> >::iterator, std::__cxx11::string&)’
       if (find(species.begin(), species.end(), s) == species.end()) {
                                                 ^
In file included from /usr/include/c++/7/bits/locale_facets.h:48:0,
                 from /usr/include/c++/7/bits/basic_ios.h:37,
                 from /usr/include/c++/7/ios:44,
                 from /usr/include/c++/7/ostream:38,
                 from /usr/include/c++/7/iostream:39,
                 from gerpcol.cc:23:
/usr/include/c++/7/bits/streambuf_iterator.h:369:5: note: candidate: template<class _CharT2> typename __gnu_cxx::__enable_if<std::__is_char<_CharT2>::__value, std::istreambuf_iterator<_CharT> >::__type std::find(std::istreambuf_iterator<_CharT>, std::istreambuf_iterator<_CharT>, const _CharT2&)
     find(istreambuf_iterator<_CharT> __first,
     ^~~~
/usr/include/c++/7/bits/streambuf_iterator.h:369:5: note:   template argument deduction/substitution failed:
gerpcol.cc:154:49: note:   ‘__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char>*, std::vector<std::__cxx11::basic_string<char> > >’ is not derived from ‘std::istreambuf_iterator<_CharT>’
       if (find(species.begin(), species.end(), s) == species.end()) {
                                                 ^
gerpcol.cc: In function ‘void processMAF(std::ofstream&, ETree&, double*)’:
gerpcol.cc:197:3: error: ‘sort’ was not declared in this scope
   sort(species.begin(), species.end());
   ^~~~
gerpcol.cc:197:3: note: suggested alternative: ‘qsort’
   sort(species.begin(), species.end());
   ^~~~
   qsort
gerpcol.cc: In function ‘int main(int, char**)’:
gerpcol.cc:459:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
     system("date");
     ~~~~~~^~~~~~~~
Makefile:14: recipe for target 'gerpcol.o' failed
make: *** [gerpcol.o] Error 1

Anyone have any idea how to resolve this issue.

[colindaven]

No idea, but you shouldn't need sudo for make

Try also make -j 4 for multiple cores

Answer 1

[an.gorohovski]

Hello, You have to add into files etree.cc, gerpcol.cc, and gerpelem.cc one line :

#include <cstdlib>

and run:

$ make clean
$ make

It's all . Good luck!

Alessandro

[musha]

If you still have problems after adding #include <cstdlib>, try to add also these lines to the same files:

#include <algorithm>

#include <cstring>