search

COMBINE-lab / matryoshka

Methods for the automated discovery of hierarchically-structured chromatin domains
5 stars 1 forks source link

problem in installing the matryoshka software #2

Closed ancient-learner closed 6 years ago

ancient-learner commented 8 years ago

Hi I have been trying to install the software by following the instructions. after installing gcc and boost through brew install when i try to compile matryoshka i am getting the following error

g++-5 -std=c++11 -w -lboost_system -lboost_iostreams -lboost_program_options -L /usr/local/Cellar/boost/1.60.0_1/lib/ -I include/ -I /usr/local/Cellar/boost/1.60.0_1/include/ -O3 -o binaries/matryoshka-linux-x64 src/*.cpp

In file included from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/resolve.hpp:26,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/push.hpp:24,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/chain.hpp:29,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from src/MatryoshkaUtil.cpp:15:
/usr/local/Cellar/boost/1.60.0_1/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
 # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
                                                                               ^
In file included from /usr/local/Cellar/boost/1.60.0_1/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/resolve.hpp:26,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/push.hpp:24,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/chain.hpp:29,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from src/MatryoshkaUtil.cpp:15:
/usr/local/Cellar/boost/1.60.0_1/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
In file included from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/resolve.hpp:26,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/push.hpp:24,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/chain.hpp:29,
                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from src/MatryoshkaUtil.cpp:15:
/usr/local/Cellar/boost/1.60.0_1/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
Undefined symbols for architecture x86_64:
  "boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
      boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*) in ccbCPx65.o
  "boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)", referenced from:
      boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int) in ccbCPx65.o
  "boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)", referenced from:
      _main in ccbCPx65.o
  "boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
      void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long) in ccbCPx65.o
      void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long) in ccbCPx65.o
      void boost::program_options::validate<unsigned long, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned long*, long) in ccbCPx65.o
  "boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)", referenced from:
      boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int) in ccbCPx65.o
  "boost::program_options::arg[abi:cxx11]", referenced from:
      boost::program_options::typed_value<int, char>::name() const in ccbCPx65.o
      boost::program_options::typed_value<bool, char>::name() const in ccbCPx65.o
      boost::program_options::typed_value<unsigned long, char>::name() const in ccbCPx65.o
      boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const in ccbCPx65.o
      boost::program_options::typed_value<double, char>::name() const in ccbCPx65.o
  "boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)", referenced from:
      boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>) in ccbCPx65.o
  "boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)", referenced from:
      boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*) in ccbCPx65.o
  "boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)", referenced from:
      boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const in ccbCPx65.o
  "boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)", referenced from:
      boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const in ccbCPx65.o
  "boost::program_options::operator<<(std::basic_ostream<char, std::char_traits<char> >&, boost::program_options::options_description const&)", referenced from:
      _main in ccbCPx65.o
  "boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const", referenced from:
      vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> in ccbCPx65.o
      vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> > in ccbCPx65.o
      vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error> in ccbCPx65.o
      vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> > in ccbCPx65.o
      vtable for boost::program_options::validation_error in ccbCPx65.o
      vtable for boost::program_options::invalid_option_value in ccbCPx65.o
  "boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const", referenced from:
      vtable for boost::program_options::typed_value<double, char> in ccbCPx65.o
      vtable for boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char> in ccbCPx65.o
      vtable for boost::program_options::typed_value<unsigned long, char> in ccbCPx65.o
      vtable for boost::program_options::typed_value<bool, char> in ccbCPx65.o
      vtable for boost::program_options::typed_value<int, char> in ccbCPx65.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
laraib85 commented 8 years ago

Hi, It seems the issue is because of difference in the boost library versions. I used version 1.59. They are not compatible. Try compiling using the older version. Also, the binaries are now available in the first release, you can use those too.

ancient-learner commented 8 years ago

I have used the binary to run matryoshka. one particular problem that i am facing now is that for a specific chromosome the tad size at level 1 is too large (70mb). it is technically not possible. I am wondering what can be done. our model organism is mouse.

laraib85 commented 8 years ago

There is a gamma Min option as well (just like that gamma Max one). You can set it to a larger value, which will result in smaller domains at the top level.