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fwhelan / coinfinder

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.
GNU General Public License v3.0
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ld: symbol(s) not found for architecture x86_64 when Linking CXX executable coinfinder #43

Closed 83035706yf closed 3 years ago

83035706yf commented 3 years ago

Hi, @fwhelan

I was installing coinfinder on my macOS. I've downloaded the code, switched my compiler to gcc via cmake -DCMAKE_BUILD_TYPE=Release . and successfully compiled files by cmake -DCMAKE_BUILD_TYPE=Release .. However, When I tried to build the files, I got

Undefined symbols for architecture x86_64: "__ZN3Gml3runER7DataSetRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE", referenced from: _main in main.cpp.o "__ZNKSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE5rfindEcm", referenced from: __ZNK5boost10filesystem4path9extensionEv in libboost_filesystem-mt.a(path.o) __ZNK5boost10filesystem4path4stemEv in libboost_filesystem-mt.a(path.o) "__ZNKSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE7compareEmmPKcm", referenced from: __ZNK5boost10filesystem4path5beginEv in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path25m_path_iterator_decrementERNS1_8iteratorE in libboost_filesystem-mt.a(path.o) "__ZNKSt3__120__vector_base_commonILb1EE20__throw_length_errorEv", referenced from: __ZNSt3__16vectorIN5boost10filesystem18directory_iteratorENS_9allocatorIS3_EEE9push_backEOS3_ in libboost_filesystem-mt.a(directory.o) "__ZNKSt3__121__basic_string_commonILb1EE20__throw_length_errorEv", referenced from: __ZNK5boost6system6detail22generic_error_category7messageEi in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem4path6assignIPcEERS1_T_S5_ in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem6detail19temp_directory_pathEPNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZNK5boost6system6detail21system_error_category7messageEi in libboost_filesystem-mt.a(operations.o) __ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE23__append_forward_unsafeIPKcEERS5_T_SA_ in libboost_filesystem-mt.a(operations.o) __ZNK5boost6system6detail22generic_error_category7messageEi in libboost_filesystem-mt.a(exception.o) __ZN5boost10filesystem10emit_errorEiPNS_6system10error_codeEPKc in libboost_filesystem-mt.a(exception.o) ... "__ZNKSt3__16locale9use_facetERNS0_2idE", referenced from: __ZN5boost10filesystem4path7codecvtEv in libboost_filesystem-mt.a(path.o) "__ZNSt13runtime_errorC2ERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE", referenced from: __ZN5boost10filesystem16filesystem_errorC2ERKNSt3__112basic_stringIcNS2_11char_traitsIcEENS2_9allocatorIcEEEENS_6system10error_codeE in libboost_filesystem-mt.a(exception.o) __ZN5boost10filesystem16filesystem_errorC2ERKNSt3__112basic_stringIcNS2_11char_traitsIcEENS2_9allocatorIcEEEERKNS0_4pathENS_6system10error_codeE in libboost_filesystem-mt.a(exception.o) __ZN5boost10filesystem16filesystem_errorC2ERKNSt3__112basic_stringIcNS2_11char_traitsIcEENS2_9allocatorIcEEEERKNS0_4pathESD_NS_6system10error_codeE in libboost_filesystem-mt.a(exception.o) "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE5eraseEmm", referenced from: __ZN5boost10filesystem4path27m_erase_redundant_separatorEm in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path15remove_filenameEv in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path25remove_trailing_separatorEv in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path17replace_extensionERKS1_ in libboost_filesystem-mt.a(path.o) __ZNK5boost10filesystem4path16lexically_normalEv in libboost_filesystem-mt.a(path.o) "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE6appendEPKc", referenced from: __ZNK5boost6system12system_error4whatEv in libboost_filesystem-mt.a(exception.o) __ZNK5boost10filesystem16filesystem_error4whatEv in libboost_filesystem-mt.a(exception.o) __ZN5boost10filesystem4pathdVEPKc in libboost_filesystem-mt.a(path.o) __ZNK5boost10filesystem4path9root_pathEv in libboost_filesystem-mt.a(path.o) "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE6appendEPKcm", referenced from: __ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE23__append_forward_unsafeIPKcEERS5_T_SA_ in libboost_filesystem-mt.a(operations.o) __ZNK5boost6system12system_error4whatEv in libboost_filesystem-mt.a(exception.o) __ZNK5boost10filesystem16filesystem_error4whatEv in libboost_filesystem-mt.a(exception.o) __ZN5boost10filesystem4pathdVERKS1_ in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4pathdVEPKc in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path17replace_extensionERKS1_ in libboost_filesystem-mt.a(path.o) __ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE23__append_forward_unsafeIPKcEERS5_T_SA_ in libboost_filesystem-mt.a(path.o) ... "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE6assignEPKc", referenced from: __ZN5boost10filesystem6detail12current_pathEPNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZNK5boost6system12system_error4whatEv in libboost_filesystem-mt.a(exception.o) __ZNK5boost10filesystem16filesystem_error4whatEv in libboost_filesystem-mt.a(exception.o) __ZNK5boost10filesystem4path5beginEv in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path25m_path_iterator_decrementERNS1_8iteratorE in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem6detail28directory_iterator_constructERNS0_18directory_iteratorERKNS0_4pathEjPNS_6system10error_codeE in libboost_filesystem-mt.a(directory.o) __ZN5boost10filesystem6detail28directory_iterator_incrementERNS0_18directory_iteratorEPNS_6system10error_codeE in libboost_filesystem-mt.a(directory.o) ... "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE9__grow_byEmmmmmm", referenced from: __ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE23__append_forward_unsafeIPKcEERS5_T_SA_ in libboost_filesystem-mt.a(operations.o) __ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE23__append_forward_unsafeIPKcEERS5_T_SA_ in libboost_filesystem-mt.a(path.o) "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE9push_backEc", referenced from: __ZN5boost10filesystem4pathdVERKS1_ in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path28m_append_separator_if_neededEv in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4pathdVEPKc in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path17replace_extensionERKS1_ in libboost_filesystem-mt.a(path.o) "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEC1ERKS5_", referenced from: __ZN5boost10filesystem6detail8absoluteERKNS0_4pathES4_PNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem6detail9canonicalERKNS0_4pathES4_PNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem6detail4copyERKNS0_4pathES4_jPNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem6detail12initial_pathEPNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem6detail16weakly_canonicalERKNS0_4pathEPNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem6detail15system_completeERKNS0_4pathEPNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem16filesystem_errorC2ERKNSt3__112basic_stringIcNS2_11char_traitsIcEENS2_9allocatorIcEEEERKNS0_4pathENS_6system10error_codeE in libboost_filesystem-mt.a(exception.o) ... "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEC1ERKS5_mmRKS4_", referenced from: __ZNK5boost10filesystem4path5beginEv in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path25m_path_iterator_incrementERNS1_8iteratorE in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path25m_path_iterator_decrementERNS1_8iteratorE in libboost_filesystem-mt.a(path.o) "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEaSERKS5_", referenced from: __ZN5boost10filesystem6detail9canonicalERKNS0_4pathES4_PNS_6system10error_codeE in libboost_filesystem-mt.a(operations.o) __ZN5boost10filesystem16filesystem_erroraSERKS1_ in libboost_filesystem-mt.a(exception.o) __ZNK5boost10filesystem4path5beginEv in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path25m_path_iterator_incrementERNS1_8iteratorE in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path25m_path_iterator_decrementERNS1_8iteratorE in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem11path_traits8dispatchERKNS0_15directory_entryERNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERKNS5_7codecvtIwc11__mbstate_tEE in libboost_filesystem-mt.a(directory.o) __ZN5boost10filesystem11path_traits8dispatchERKNS0_15directory_entryERNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE in libboost_filesystem-mt.a(directory.o) ... "__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEaSEc", referenced from: __ZN5boost10filesystem4path25m_path_iterator_incrementERNS1_8iteratorE in libboost_filesystem-mt.a(path.o) "__ZNSt3__16locale14__install_ctorERKS0_PNS0_5facetEl", referenced from: __ZN12_GLOBAL__N_111path_localeEv in libboost_filesystem-mt.a(path.o) "__ZNSt3__16locale2id5__getEv", referenced from: __ZN12_GLOBAL__N_111path_localeEv in libboost_filesystem-mt.a(path.o) "__ZNSt3__16locale5facet16__on_zero_sharedEv", referenced from: __ZTVN5boost10filesystem6detail18utf8_codecvt_facetE in libboost_filesystem-mt.a(utf8_codecvt_facet.o) "__ZNSt3__16localeC1ERKS0_", referenced from: __ZN5boost10filesystem4path5imbueERKNSt3__16localeE in libboost_filesystem-mt.a(path.o) "__ZNSt3__16localeC1Ev", referenced from: __ZN12_GLOBAL__N_111path_localeEv in libboost_filesystem-mt.a(path.o) "__ZNSt3__16localeD1Ev", referenced from: __ZN12_GLOBAL__N_111path_localeEv in libboost_filesystem-mt.a(path.o) __ZN5boost10filesystem4path5imbueERKNSt3__16localeE in libboost_filesystem-mt.a(path.o) "__ZNSt3__16localeaSERKS0_", referenced from: __ZN5boost10filesystem4path5imbueERKNSt3__16localeE in libboost_filesystem-mt.a(path.o) "__ZNSt3__17codecvtIwc11__mbstate_tE2idE", referenced from: __ZN5boost10filesystem4path7codecvtEv in libboost_filesystem-mt.a(path.o) __ZN12_GLOBAL__N_111path_localeEv in libboost_filesystem-mt.a(path.o) "__ZNSt3__17codecvtIwc11__mbstate_tEC2Em", referenced from: __ZN5boost10filesystem6detail18utf8_codecvt_facetC2Em in libboost_filesystem-mt.a(utf8_codecvt_facet.o) __ZN5boost10filesystem6detail18utf8_codecvt_facetC1Em in libboost_filesystem-mt.a(utf8_codecvt_facet.o) "__ZNSt3__17codecvtIwc11__mbstate_tED2Ev", referenced from: __ZN5boost10filesystem6detail18utf8_codecvt_facetD2Ev in libboost_filesystem-mt.a(utf8_codecvt_facet.o) __ZN5boost10filesystem6detail18utf8_codecvt_facetD1Ev in libboost_filesystem-mt.a(utf8_codecvt_facet.o) __ZN5boost10filesystem6detail18utf8_codecvt_facetD0Ev in libboost_filesystem-mt.a(utf8_codecvt_facet.o) "__ZTINSt3__17codecvtIwc11__mbstate_tEE", referenced from: __ZTIN5boost10filesystem6detail18utf8_codecvt_facetE in libboost_filesystem-mt.a(utf8_codecvt_facet.o) ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status make[2]: *** [coinfinder] Error 1 make[1]: *** [CMakeFiles/coinfinder.dir/all] Error 2 make: *** [all] Error 2

Any help would be really appreciated!

fwhelan commented 3 years ago

Hello! Apologies for not getting back to you sooner. I would recommend trying to install coinfinder via conda if that option is available to you?

fwhelan commented 3 years ago

Closing due to inactivity; please re-open if you'd like to revisit.