{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/matryoshka/issues/2","repository_url":"https://api.github.com/repos/COMBINE-lab/matryoshka","labels_url":"https://api.github.com/repos/COMBINE-lab/matryoshka/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/matryoshka/issues/2/comments","events_url":"https://api.github.com/repos/COMBINE-lab/matryoshka/issues/2/events","html_url":"https://github.com/COMBINE-lab/matryoshka/issues/2","id":130953741,"number":2,"title":"problem in installing the matryoshka software","user":{"login":"ancient-learner","id":5870207,"avatar_url":"https://avatars.githubusercontent.com/u/5870207?v=3","gravatar_id":"","url":"https://api.github.com/users/ancient-learner","html_url":"https://github.com/ancient-learner","followers_url":"https://api.github.com/users/ancient-learner/followers","following_url":"https://api.github.com/users/ancient-learner/following{/other_user}","gists_url":"https://api.github.com/users/ancient-learner/gists{/gist_id}","starred_url":"https://api.github.com/users/ancient-learner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ancient-learner/subscriptions","organizations_url":"https://api.github.com/users/ancient-learner/orgs","repos_url":"https://api.github.com/users/ancient-learner/repos","events_url":"https://api.github.com/users/ancient-learner/events{/privacy}","received_events_url":"https://api.github.com/users/ancient-learner/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-02-03T08:42:22Z","updated_at":"2016-02-19T04:38:02Z","closed_at":null,"body":"Hi\r\nI 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\r\n\r\n`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`\r\n\r\n\r\n```\r\nIn file included from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/resolve.hpp:26,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/push.hpp:24,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/chain.hpp:29,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/filtering_streambuf.hpp:17,\r\n                 from src/MatryoshkaUtil.cpp:15:\r\n/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\r\n # pragma message(\"NOTE: Use of this header (bool_trait_def.hpp) is deprecated\")\r\n                                                                               ^\r\nIn file included from /usr/local/Cellar/boost/1.60.0_1/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/is_dereferenceable.hpp:12,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/resolve.hpp:26,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/push.hpp:24,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/chain.hpp:29,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/filtering_streambuf.hpp:17,\r\n                 from src/MatryoshkaUtil.cpp:15:\r\n/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\r\n # pragma message(\"NOTE: Use of this header (template_arity_spec.hpp) is deprecated\")\r\n                                                                                    ^\r\nIn file included from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/resolve.hpp:26,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/detail/push.hpp:24,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/chain.hpp:29,\r\n                 from /usr/local/Cellar/boost/1.60.0_1/include/boost/iostreams/filtering_streambuf.hpp:17,\r\n                 from src/MatryoshkaUtil.cpp:15:\r\n/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\r\n # pragma message(\"NOTE: Use of this header (template_arity_spec.hpp) is deprecated\")\r\n                                                                                    ^\r\nUndefined symbols for architecture x86_64:\r\n  \"boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)\", referenced from:\r\n      boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*) in ccbCPx65.o\r\n  \"boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)\", referenced from:\r\n      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\r\n  \"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:\r\n      _main in ccbCPx65.o\r\n  \"boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)\", referenced from:\r\n      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\r\n      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\r\n      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\r\n  \"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:\r\n      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\r\n  \"boost::program_options::arg[abi:cxx11]\", referenced from:\r\n      boost::program_options::typed_value<int, char>::name() const in ccbCPx65.o\r\n      boost::program_options::typed_value<bool, char>::name() const in ccbCPx65.o\r\n      boost::program_options::typed_value<unsigned long, char>::name() const in ccbCPx65.o\r\n      boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const in ccbCPx65.o\r\n      boost::program_options::typed_value<double, char>::name() const in ccbCPx65.o\r\n  \"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:\r\n      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\r\n  \"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:\r\n      boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*) in ccbCPx65.o\r\n  \"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:\r\n      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\r\n  \"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:\r\n      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\r\n  \"boost::program_options::operator<<(std::basic_ostream<char, std::char_traits<char> >&, boost::program_options::options_description const&)\", referenced from:\r\n      _main in ccbCPx65.o\r\n  \"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:\r\n      vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> in ccbCPx65.o\r\n      vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> > in ccbCPx65.o\r\n      vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error> in ccbCPx65.o\r\n      vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> > in ccbCPx65.o\r\n      vtable for boost::program_options::validation_error in ccbCPx65.o\r\n      vtable for boost::program_options::invalid_option_value in ccbCPx65.o\r\n  \"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:\r\n      vtable for boost::program_options::typed_value<double, char> in ccbCPx65.o\r\n      vtable for boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char> in ccbCPx65.o\r\n      vtable for boost::program_options::typed_value<unsigned long, char> in ccbCPx65.o\r\n      vtable for boost::program_options::typed_value<bool, char> in ccbCPx65.o\r\n      vtable for boost::program_options::typed_value<int, char> in ccbCPx65.o\r\nld: symbol(s) not found for architecture x86_64\r\ncollect2: error: ld returned 1 exit status\r\n```"},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/matryoshka/issues/comments/186047831","html_url":"https://github.com/COMBINE-lab/matryoshka/issues/2#issuecomment-186047831","issue_url":"https://api.github.com/repos/COMBINE-lab/matryoshka/issues/2","id":186047831,"user":{"login":"ancient-learner","id":5870207,"avatar_url":"https://avatars.githubusercontent.com/u/5870207?v=3","gravatar_id":"","url":"https://api.github.com/users/ancient-learner","html_url":"https://github.com/ancient-learner","followers_url":"https://api.github.com/users/ancient-learner/followers","following_url":"https://api.github.com/users/ancient-learner/following{/other_user}","gists_url":"https://api.github.com/users/ancient-learner/gists{/gist_id}","starred_url":"https://api.github.com/users/ancient-learner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ancient-learner/subscriptions","organizations_url":"https://api.github.com/users/ancient-learner/orgs","repos_url":"https://api.github.com/users/ancient-learner/repos","events_url":"https://api.github.com/users/ancient-learner/events{/privacy}","received_events_url":"https://api.github.com/users/ancient-learner/received_events","type":"User","site_admin":false},"created_at":"2016-02-19T04:38:02Z","updated_at":"2016-02-19T04:38:02Z","body":"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."}}