molpopgen / msstats Goto Github PK

line ending in markdown cause typo in readme.
ms format is not:

// segsites: 2 positions: 0.1 0.9 01 10

but instead:

//
segsites: 2
positions: 0.1 0.9
01
10

Dear Kevin,

I am trying to install msstats in my MacBook Pro Yosemite 10.10.5 but I am unable to do it. I don't have a computational background and I don't have any C++ knowledge.

I followed the instructions provided in GitHub: cd into the msstats directory and run ./configure. I get this:

Lucass-MacBook-Pro:msstats-master lucas$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/Users/lucas/Dropbox/puc/Softwares/msstats-master/missing: Unknown --is-lightweight' option Try /Users/lucas/Dropbox/puc/Softwares/msstats-master/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for an ANSI C-conforming const... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking whether g++ supports C++11 features by default... no
checking whether g++ supports C++11 features with -std=c++11... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for main in -lgslcblas... no
GSL BLAS runtime library not found

Also, when I write "make":

Lucass-MacBook-Pro:msstats-master lucas$ make
make: *** No targets specified and no makefile found. Stop.

Or "make install" or "sudo make install" I get:

Lucass-MacBook-Pro:msstats-master lucas$ make install
make: Nothing to be done for `install'.

Lucass-MacBook-Pro:msstats-master lucas$ sudo make install
Password:
make: Nothing to be done for `install'.

Do you have any idea of why I am unable to compile msstats?

Thank you very much in advance
Best regards,
Lucas

I'm having trouble compiling msstats and I'm not familiar enough with c++ to troubleshoot. Do you have any suggestions?

Just running './configure' and 'make'

make[2]: Entering directory '/home/haekel/Desktop/msstats/src' g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -DNDEBUG -O3 -Wall -W -g -O2 -std=c++11 -MT msstats.o -MD -MP -MF .deps/msstats.Tpo -c -o msstats.o msstats.cc msstats.cc: In function ‘int main(int, char**)’: msstats.cc:166:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 0 ; i < config.size() ; ++i) ^ msstats.cc:172:25: error: no matching function for call to ‘Sequence::SimData::assign(double*, unsigned int, __gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type*, __gnu_cxx::__alloc_traits<std::allocator<int> >::value_type&)’ &d[sum],config[i]); ^ In file included from /usr/local/include/Sequence/SimData.hpp:65:0, from msstats.cc:29: /usr/local/include/Sequence/PolyTable.hpp:188:10: note: candidate: bool Sequence::PolyTable::assign(Sequence::PolyTable::const_site_iterator, Sequence::PolyTable::const_site_iterator) bool assign(PolyTable::const_site_iterator beg, ^ /usr/local/include/Sequence/PolyTable.hpp:188:10: note: candidate expects 2 arguments, 4 provided /usr/local/include/Sequence/PolyTable.hpp:197:10: note: candidate: bool Sequence::PolyTable::assign(const std::vector<double>&, const std::vector<std::__cxx11::basic_string<char> >&) bool assign( const std::vector<double> & __positions, ^ /usr/local/include/Sequence/PolyTable.hpp:197:10: note: candidate expects 2 arguments, 4 provided /usr/local/include/Sequence/PolyTable.hpp:203:10: note: candidate: bool Sequence::PolyTable::assign(std::vector<double>&&, std::vector<std::__cxx11::basic_string<char> >&&) bool assign( std::vector<double> && __positions, ^ /usr/local/include/Sequence/PolyTable.hpp:203:10: note: candidate expects 2 arguments, 4 provided msstats.cc:175:34: error: ‘RemoveInvariantColumns’ was not declared in this scope RemoveInvariantColumns(&d2); ^ msstats.cc:65:7: warning: unused variable ‘total’ [-Wunused-variable] int total = std::accumulate(config.begin(),config.end(),0,plus<int>()); ^ msstats.cc: In function ‘void calcstats(const Sequence::SimData&, const unsigned int&)’: msstats.cc:222:85: error: invalid initialization of reference of type ‘const bool&’ from expression of type ‘std::vector<double>’ while( Recombination::Disequilibrium(&d,LDSTATS,&site1,&site2,false,0,mincount)) ^ In file included from /usr/local/include/Sequence/PolySNP.hpp:80:0, from /usr/local/include/Sequence/PolySIM.hpp:41, from msstats.cc:30: /usr/local/include/Sequence/Recombination.hpp:96:38: note: in passing argument 2 of ‘std::vector<Sequence::PairwiseLDstats> Sequence::Recombination::Disequilibrium(const Sequence::PolyTable*, const bool&, const unsigned int&, const unsigned int&, double)’ std::vector<PairwiseLDstats> Disequilibrium( ^ Makefile:406: recipe for target 'msstats.o' failed make[2]: *** [msstats.o] Error 1 make[2]: Leaving directory '/home/haekel/Desktop/msstats/src' Makefile:352: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/haekel/Desktop/msstats' Makefile:292: recipe for target 'all' failed make: *** [all] Error 2

I also tried this code but it didn't help.
./configure CC=gcc CXXFLAGS='-Wno-sign-compare'