{"action":"created","issue":{"url":"https://api.github.com/repos/mlpack/mlpack/issues/804","repository_url":"https://api.github.com/repos/mlpack/mlpack","labels_url":"https://api.github.com/repos/mlpack/mlpack/issues/804/labels{/name}","comments_url":"https://api.github.com/repos/mlpack/mlpack/issues/804/comments","events_url":"https://api.github.com/repos/mlpack/mlpack/issues/804/events","html_url":"https://github.com/mlpack/mlpack/issues/804","id":185301847,"number":804,"title":"cannot build mlpack in hpc","user":{"login":"wan9c9","id":7605222,"avatar_url":"https://avatars.githubusercontent.com/u/7605222?v=3","gravatar_id":"","url":"https://api.github.com/users/wan9c9","html_url":"https://github.com/wan9c9","followers_url":"https://api.github.com/users/wan9c9/followers","following_url":"https://api.github.com/users/wan9c9/following{/other_user}","gists_url":"https://api.github.com/users/wan9c9/gists{/gist_id}","starred_url":"https://api.github.com/users/wan9c9/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wan9c9/subscriptions","organizations_url":"https://api.github.com/users/wan9c9/orgs","repos_url":"https://api.github.com/users/wan9c9/repos","events_url":"https://api.github.com/users/wan9c9/events{/privacy}","received_events_url":"https://api.github.com/users/wan9c9/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-10-26T05:39:07Z","updated_at":"2016-11-01T20:57:31Z","closed_at":null,"body":"Hello, \n\nI want to build mlpack in HPC without root privilege, but I'm facing the following errors. Please advice.\n\n 25%] Linking CXX executable ../../../../bin/mlpack_preprocess_split\ncd /Users/cwang42/workspace/tools/mlpack-2.0.3/build/src/mlpack/methods/preprocess && /opt/cmake/3.4.3/bin/cmake -E cmake_link_script CMakeFiles/mlpack_preprocess_split.dir/link.txt --verbose=1\n/opt/gcc/6.1.0/bin/c++   -fext-numeric-literals -I/Users/cwang42/opt2/usr/include  -std=c++0x -O3 -fopenmp   -L/Users/cwang42/opt2/usr/lib64 CMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o  -o ../../../../bin/mlpack_preprocess_split -rdynamic ../../../../lib/libmlpack.so.2.0 -larmadillo -lboost_program_options-mt -lboost_unit_test_framework-mt -lboost_serialization-mt -lrt -Wl,-rpath,/Users/cwang42/workspace/tools/mlpack-2.0.3/build/lib: \nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.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':\npreprocess_split_main.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x19): 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)'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.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)':\npreprocess_split_main.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to`_ZN5boost15program_options16validation_error12get_templateB5cxx11ENS1_6kind_tE'\npreprocess_split_main.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): 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)'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o: In function`boost::program_options::error_with_option_name::~error_with_option_name()':\npreprocess_split_main.cpp:(.text._ZN5boost15program_options22error_with_option_nameD2Ev[_ZN5boost15program_options22error_with_option_nameD5Ev]+0x17): undefined reference to `vtable for boost::program_options::error_with_option_name'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o: In function`void mlpack::data::Split<double, double>(arma::Mat<double> const&, arma::Row<double> const&, arma::Mat<double>&, arma::Mat<double>&, arma::Row<double>&, arma::Row<double>&, double)':\npreprocess_split_main.cpp:(.text._ZN6mlpack4data5SplitIddEEvRKN4arma3MatIT_EERKNS2_3RowIT0_EERS5_SD_RSA_SE_d[_ZN6mlpack4data5SplitIddEEvRKN4arma3MatIT_EERKNS2_3RowIT0_EERS5_SD_RSA_SE_d]+0x2a2): undefined reference to `arma::arma_rng_cxx11_instance'\npreprocess_split_main.cpp:(.text._ZN6mlpack4data5SplitIddEEvRKN4arma3MatIT_EERKNS2_3RowIT0_EERS5_SD_RSA_SE_d[_ZN6mlpack4data5SplitIddEEvRKN4arma3MatIT_EERKNS2_3RowIT0_EERS5_SD_RSA_SE_d]+0x2d6): undefined reference to`arma::arma_rng_cxx11_instance'\npreprocess_split_main.cpp:(.text._ZN6mlpack4data5SplitIddEEvRKN4arma3MatIT_EERKNS2_3RowIT0_EERS5_SD_RSA_SE_d[_ZN6mlpack4data5SplitIddEEvRKN4arma3MatIT_EERKNS2_3RowIT0_EERS5_SD_RSA_SE_d]+0x307): undefined reference to `arma::arma_rng_cxx11_instance'\npreprocess_split_main.cpp:(.text._ZN6mlpack4data5SplitIddEEvRKN4arma3MatIT_EERKNS2_3RowIT0_EERS5_SD_RSA_SE_d[_ZN6mlpack4data5SplitIddEEvRKN4arma3MatIT_EERKNS2_3RowIT0_EERS5_SD_RSA_SE_d]+0x7c3): undefined reference to`arma::arma_rng_cxx11_instance'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o: In function `void mlpack::data::Split<double>(arma::Mat<double> const&, arma::Mat<double>&, arma::Mat<double>&, double)':\npreprocess_split_main.cpp:(.text._ZN6mlpack4data5SplitIdEEvRKN4arma3MatIT_EERS5_S8_d[_ZN6mlpack4data5SplitIdEEvRKN4arma3MatIT_EERS5_S8_d]+0x262): undefined reference to`arma::arma_rng_cxx11_instance'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:preprocess_split_main.cpp:(.text._ZN6mlpack4data5SplitIdEEvRKN4arma3MatIT_EERS5_S8_d[_ZN6mlpack4data5SplitIdEEvRKN4arma3MatIT_EERS5_S8_d]+0x296): more undefined references to `arma::arma_rng_cxx11_instance' follow\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o: In function`_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameB5cxx11Ev':\npreprocess_split_main.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameB5cxx11Ev]+0xb): undefined reference to `_ZN5boost15program_options3argB5cxx11E'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o: In function`_ZNK5boost15program_options11typed_valueIdcE4nameB5cxx11Ev':\npreprocess_split_main.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIdcE4nameB5cxx11Ev]+0xb): undefined reference to `_ZN5boost15program_options3argB5cxx11E'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o: In function`boost::program_options::error_with_option_name::error_with_option_name(boost::program_options::error_with_option_name const&)':\npreprocess_split_main.cpp:(.text._ZN5boost15program_options22error_with_option_nameC2ERKS1_[_ZN5boost15program_options22error_with_option_nameC5ERKS1_]+0x2d): undefined reference to `vtable for boost::program_options::error_with_option_name'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o: In function`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)':\npreprocess_split_main.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x4fc): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x20): undefined reference to`boost::program_options::error_with_option_name::what() const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x28): undefined reference to`boost::program_options::error_with_option_name::what() const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x20): undefined reference to`boost::program_options::error_with_option_name::what() const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x28): undefined reference to`boost::program_options::error_with_option_name::what() const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTIN5boost15program_options16validation_errorE[_ZTIN5boost15program_options16validation_errorE]+0x10): undefined reference to`typeinfo for boost::program_options::error_with_option_name'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to`boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to`boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `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'\nCMakeFiles/mlpack_preprocess_split.dir/preprocess_split_main.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to`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'\n../../../../lib/libmlpack.so.2.0: undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'\n../../../../lib/libmlpack.so.2.0: undefined reference to`boost::archive::archive_exception::archive_exception(boost::archive::archive_exception const&)'\n../../../../lib/libmlpack.so.2.0: undefined reference to `boost::archive::basic_xml_oarchive<boost::archive::xml_oarchive>::save_override(boost::archive::class_id_type const&)'\n../../../../lib/libmlpack.so.2.0: 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&)'\n../../../../lib/libmlpack.so.2.0: undefined reference to `boost::program_options::detail::cmdline::get_canonical_option_prefix()'\n../../../../lib/libmlpack.so.2.0: undefined reference to`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&>)'\n../../../../lib/libmlpack.so.2.0: undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'\n../../../../lib/libmlpack.so.2.0: undefined reference to`boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\ncollect2: error: ld returned 1 exit status\nmake[2]: **\\* [bin/mlpack_preprocess_split] Error 1\nmake[2]: Leaving directory `/Users/cwang42/workspace/tools/mlpack-2.0.3/build'\nmake[1]: *** [src/mlpack/methods/preprocess/CMakeFiles/mlpack_preprocess_split.dir/all] Error 2\nmake[1]: Leaving directory`/Users/cwang42/workspace/tools/mlpack-2.0.3/build'\nmake: **\\* [all] Error 2\n\nThanks a lot,\n\nChao\n"},"comment":{"url":"https://api.github.com/repos/mlpack/mlpack/issues/comments/257694452","html_url":"https://github.com/mlpack/mlpack/issues/804#issuecomment-257694452","issue_url":"https://api.github.com/repos/mlpack/mlpack/issues/804","id":257694452,"user":{"login":"rcurtin","id":1845039,"avatar_url":"https://avatars.githubusercontent.com/u/1845039?v=3","gravatar_id":"","url":"https://api.github.com/users/rcurtin","html_url":"https://github.com/rcurtin","followers_url":"https://api.github.com/users/rcurtin/followers","following_url":"https://api.github.com/users/rcurtin/following{/other_user}","gists_url":"https://api.github.com/users/rcurtin/gists{/gist_id}","starred_url":"https://api.github.com/users/rcurtin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rcurtin/subscriptions","organizations_url":"https://api.github.com/users/rcurtin/orgs","repos_url":"https://api.github.com/users/rcurtin/repos","events_url":"https://api.github.com/users/rcurtin/events{/privacy}","received_events_url":"https://api.github.com/users/rcurtin/received_events","type":"User","site_admin":false},"created_at":"2016-11-01T20:57:31Z","updated_at":"2016-11-01T20:57:31Z","body":"Hi there, sorry for the slow response---I was traveling.  When you re-ran CMake, did you remove `CMakeLists.txt` from the build directory first?  I think that it will not re-search for Boost libraries even if you specify `Boost_NO_BOOST_CMAKE`, if it has already found it.\r\n\r\nIf you did remove `CMakeLists.txt`, can you provide the output of `VERBOSE=1 make`?  Thanks."}}
{"actor":{"display_login":"rcurtin"}}