Question: Gerp++ installation error
gravatar for Abdul Rafay Khan
12 months ago by
Karachi, PK
Abdul Rafay Khan1.1k wrote:

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
g++ -Wall -W -pedantic -O4 -c In member function ‘Vec<char> Mseq::getAlignment(Seq::size_type, Seq::size_type) const’: warning: variable ‘X_end’ set but not used [-Wunused-but-set-variable]
                X_end = X.getEnd(),
                ^~~~~ warning: variable ‘Y_end’ set but not used [-Wunused-but-set-variable]
                Y_end = Y.getEnd();
g++ -Wall -W -pedantic -O4 -c
g++ -Wall -W -pedantic -O4 -c
g++ -Wall -W -pedantic -O4 -c
g++ -Wall -W -pedantic -O4 -c In function ‘void estimateFreqs(std::vector<std::__cxx11::basic_string<char> >&, double*)’: 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,
/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: 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()) {
                                                 ^ In function ‘void processMAF(std::ofstream&, ETree&, double*)’: error: ‘sort’ was not declared in this scope
   sort(species.begin(), species.end());
   ^~~~ note: suggested alternative: ‘qsort’
   sort(species.begin(), species.end());
   qsort In function ‘int main(int, char**)’: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
Makefile:14: recipe for target 'gerpcol.o' failed
make: *** [gerpcol.o] Error 1

Anyone have any idea how to resolve this issue.

snp gerp gerp2 gerp++ • 405 views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 12 months ago by Abdul Rafay Khan1.1k

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

Try also make -j 4 for multiple cores

ADD REPLYlink written 12 months ago by colindaven1.9k

Tried via conda?

ADD REPLYlink written 12 months ago by ATpoint28k
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