{"action":"created","issue":{"url":"https://api.github.com/repos/TGAC/KAT/issues/67","repository_url":"https://api.github.com/repos/TGAC/KAT","labels_url":"https://api.github.com/repos/TGAC/KAT/issues/67/labels{/name}","comments_url":"https://api.github.com/repos/TGAC/KAT/issues/67/comments","events_url":"https://api.github.com/repos/TGAC/KAT/issues/67/events","html_url":"https://github.com/TGAC/KAT/issues/67","id":194082741,"number":67,"title":"kat-plot_density.o: In function `boost::filesystem::exists(boost::filesystem::path const&)': /usr/include/boost/filesystem/operations.hpp:446: undefined reference to `boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'","user":{"login":"mmokrejs","id":3297852,"avatar_url":"https://avatars.githubusercontent.com/u/3297852?v=3","gravatar_id":"","url":"https://api.github.com/users/mmokrejs","html_url":"https://github.com/mmokrejs","followers_url":"https://api.github.com/users/mmokrejs/followers","following_url":"https://api.github.com/users/mmokrejs/following{/other_user}","gists_url":"https://api.github.com/users/mmokrejs/gists{/gist_id}","starred_url":"https://api.github.com/users/mmokrejs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmokrejs/subscriptions","organizations_url":"https://api.github.com/users/mmokrejs/orgs","repos_url":"https://api.github.com/users/mmokrejs/repos","events_url":"https://api.github.com/users/mmokrejs/events{/privacy}","received_events_url":"https://api.github.com/users/mmokrejs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-12-07T15:38:37Z","updated_at":"2016-12-07T17:10:29Z","closed_at":null,"body":"Hi,\r\n  when trying to compile current git HEAD on my Gentoo Linux box I get:\r\n```  CXXLD    kat\r\nkat-plot_density.o: In function `boost::filesystem::exists(boost::filesystem::path const&)':\r\n/usr/include/boost/filesystem/operations.hpp:446: undefined reference to `boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'\r\nkat-plot_density.o: In function `boost::filesystem::symlink_status(boost::filesystem::path const&)':\r\n/usr/include/boost/filesystem/operations.hpp:441: undefined reference to `boost::filesystem::detail::symlink_status(boost::filesystem::path const&, boost::system::error_code*)'\r\nkat-plot_density.o: In function `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':\r\n/usr/include/boost/program_options/detail/value_semantic.hpp:167: undefined reference to `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)'\r\nkat-plot_density.o: In function `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)':\r\n/usr/include/boost/program_options/errors.hpp:373: undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'\r\n/usr/include/boost/program_options/errors.hpp:373: undefined reference to `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)'\r\nkat-plot_density.o: In function `boost::program_options::typed_value<unsigned short, char>::name() const':\r\n/usr/include/boost/program_options/detail/value_semantic.hpp:19: undefined reference to `boost::program_options::arg[abi:cxx11]'\r\nkat-plot_density.o: In function `boost::program_options::typed_value<unsigned long, char>::name() const':\r\n/usr/include/boost/program_options/detail/value_semantic.hpp:19: undefined reference to `boost::program_options::arg[abi:cxx11]'\r\nkat-plot_density.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const':\r\n/usr/include/boost/program_options/detail/value_semantic.hpp:19: undefined reference to `boost::program_options::arg[abi:cxx11]'\r\nkat-plot_density.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':\r\n/usr/include/boost/program_options/detail/value_semantic.hpp:19: undefined reference to `boost::program_options::arg[abi:cxx11]'\r\nkat-plot_density.o: In function `boost::program_options::typed_value<boost::filesystem::path, char>::name() const':\r\n/usr/include/boost/program_options/detail/value_semantic.hpp:19: undefined reference to `boost::program_options::arg[abi:cxx11]'\r\nkat-plot_density.o: In function `boost::program_options::error_with_option_name::~error_with_option_name()':\r\n/usr/include/boost/program_options/errors.hpp:119: undefined reference to `vtable for boost::program_options::error_with_option_name'\r\nkat-plot_density.o: In function `boost::program_options::error_with_option_name::~error_with_option_name()':\r\n/usr/include/boost/program_options/errors.hpp:119: undefined reference to `vtable for boost::program_options::error_with_option_name'\r\n/usr/include/boost/program_options/errors.hpp:119: undefined reference to `vtable for boost::program_options::error_with_option_name'\r\n/usr/include/boost/program_options/errors.hpp:119: undefined reference to `vtable for boost::program_options::error_with_option_name'\r\n/usr/include/boost/program_options/errors.hpp:119: undefined reference to `vtable for boost::program_options::error_with_option_name'\r\nkat-plot_density.o:/usr/include/boost/program_options/errors.hpp:119: more undefined references to `vtable for boost::program_options::error_with_option_name' follow\r\nkat-plot_density.o: In function `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> > > > boost::program_options::to_internal<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(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&)':\r\n/usr/include/boost/program_options/detail/convert.hpp:79: undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nkat-plot_density.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':\r\n/usr/include/boost/program_options/detail/parsers.hpp:44: undefined reference to `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&)'\r\nkat-plot_density.o: In function `boost::program_options::basic_command_line_parser<char>::run()':\r\n/usr/include/boost/program_options/detail/parsers.hpp:108: undefined reference to `boost::program_options::detail::cmdline::get_canonical_option_prefix()'\r\n/usr/include/boost/program_options/detail/parsers.hpp:109: undefined reference to `boost::program_options::detail::cmdline::run()'\r\nkat-plot_density.o: In function `boost::program_options::variables_map::~variables_map()':\r\n/usr/include/boost/program_options/variables_map.hpp:146: undefined reference to `vtable for boost::program_options::variables_map'\r\n```\r\n\r\nI am just guessing here but ... it seems the Makefile does not refer to libboost_filesystem.{a,so} files:\r\n\r\n$  grep BOOST src/Makefile\r\nBOOST_CHRONO_LIB = -lboost_chrono-mt\r\nBOOST_CHRONO_STATIC_LIB = /usr/lib64/libboost_chrono.a\r\nBOOST_CPPFLAGS = -I/usr/include\r\nBOOST_FILESYSTEM_LIB = -lboost_filesystem-mt\r\nBOOST_FILESYSTEM_STATIC_LIB = \r\nBOOST_LDFLAGS = -L/usr/lib64\r\nBOOST_PROGRAM_OPTIONS_LIB = -lboost_program_options-mt\r\nBOOST_PROGRAM_OPTIONS_STATIC_LIB = \r\nBOOST_STATIC_LIBS = /usr/lib64/libboost_timer.a /usr/lib64/libboost_chrono.a -lrt   /usr/lib64/libboost_system.a \r\nBOOST_SYSTEM_LIB = -lboost_system-mt\r\nBOOST_SYSTEM_STATIC_LIB = /usr/lib64/libboost_system.a\r\nBOOST_TIMER_LIB = -lboost_timer-mt\r\nBOOST_TIMER_STATIC_LIB = /usr/lib64/libboost_timer.a\r\n$\r\n\r\nIs my boost-1.62 too new?"},"comment":{"url":"https://api.github.com/repos/TGAC/KAT/issues/comments/265508302","html_url":"https://github.com/TGAC/KAT/issues/67#issuecomment-265508302","issue_url":"https://api.github.com/repos/TGAC/KAT/issues/67","id":265508302,"user":{"login":"mmokrejs","id":3297852,"avatar_url":"https://avatars.githubusercontent.com/u/3297852?v=3","gravatar_id":"","url":"https://api.github.com/users/mmokrejs","html_url":"https://github.com/mmokrejs","followers_url":"https://api.github.com/users/mmokrejs/followers","following_url":"https://api.github.com/users/mmokrejs/following{/other_user}","gists_url":"https://api.github.com/users/mmokrejs/gists{/gist_id}","starred_url":"https://api.github.com/users/mmokrejs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmokrejs/subscriptions","organizations_url":"https://api.github.com/users/mmokrejs/orgs","repos_url":"https://api.github.com/users/mmokrejs/repos","events_url":"https://api.github.com/users/mmokrejs/events{/privacy}","received_events_url":"https://api.github.com/users/mmokrejs/received_events","type":"User","site_admin":false},"created_at":"2016-12-07T17:10:28Z","updated_at":"2016-12-07T17:10:28Z","body":"Thank you but I am trying to make a package for KAT to be included in Gentoo ( https://cgit.gentoo.org/proj/sci.git/commit/sci-biology/kat ), so I need to find a way to integrate it using standard packages.\r\n\r\nHave just opened https://bugs.gentoo.org/show_bug.cgi?id=601914"}}
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