Temporary header file '/tmp/NyLyVFOGg0/dump1.h' with the following content will be compiled to create GCC translation unit dump: // add defines #define __STDC_VERSION__ 201710L #define _GXX_NULLPTR_T #define CLUTTER_ENABLE_COMPOSITOR_API 1 #define _REGEX_NELTS(n) #define _Atomic #define PACKED #define getaddrinfo_a(a,b,c,d) // add includes #include "/usr/include/libMems/AbstractGappedAlignment.h" #include "/usr/include/libMems/AbstractMatch.h" #include "/usr/include/libMems/Aligner.h" #include "/usr/include/libMems/Backbone.h" #include "/usr/include/libMems/CompactGappedAlignment.h" #include "/usr/include/libMems/DNAFileSML.h" #include "/usr/include/libMems/DNAMemorySML.h" #include "/usr/include/libMems/DenseAbstractMatch.h" #include "/usr/include/libMems/DistanceMatrix.h" #include "/usr/include/libMems/FileSML.h" #include "/usr/include/libMems/Files.h" #include "/usr/include/libMems/GappedAligner.h" #include "/usr/include/libMems/GappedAlignment.h" #include "/usr/include/libMems/GreedyBreakpointElimination.h" #include "/usr/include/libMems/HomologyHMM/algebras.h" #include "/usr/include/libMems/HomologyHMM/dptables.h" #include "/usr/include/libMems/HomologyHMM/homology.h" #include "/usr/include/libMems/HomologyHMM/parameters.h" #include "/usr/include/libMems/HybridAbstractMatch.h" #include "/usr/include/libMems/Interval.h" #include "/usr/include/libMems/IntervalList.h" #include "/usr/include/libMems/Islands.h" #include "/usr/include/libMems/LCB.h" #include "/usr/include/libMems/MaskedMemHash.h" #include "/usr/include/libMems/Match.h" #include "/usr/include/libMems/MatchFinder.h" #include "/usr/include/libMems/MatchHashEntry.h" #include "/usr/include/libMems/MatchList.h" #include "/usr/include/libMems/MatchProjectionAdapter.h" #include "/usr/include/libMems/Matrix.h" #include "/usr/include/libMems/MemHash.h" #include "/usr/include/libMems/Memory.h" #include "/usr/include/libMems/MemorySML.h" #include "/usr/include/libMems/MuscleInterface.h" #include "/usr/include/libMems/NumericMatrix.h" #include "/usr/include/libMems/PairwiseMatchAdapter.h" #include "/usr/include/libMems/PairwiseMatchFinder.h" #include "/usr/include/libMems/PhyloTree.h" #include "/usr/include/libMems/ProgressiveAligner.h" #include "/usr/include/libMems/RepeatHash.h" #include "/usr/include/libMems/RepeatMatch.h" #include "/usr/include/libMems/RepeatMatchList.h" #include "/usr/include/libMems/Scoring.h" #include "/usr/include/libMems/SeedMasks.h" #include "/usr/include/libMems/SeedOccurrenceList.h" #include "/usr/include/libMems/SlotAllocator.h" #include "/usr/include/libMems/SortedMerList.h" #include "/usr/include/libMems/SparseAbstractMatch.h" #include "/usr/include/libMems/SubstitutionMatrix.h" #include "/usr/include/libMems/SuperInterval.h" #include "/usr/include/libMems/TreeUtilities.h" #include "/usr/include/libMems/UngappedLocalAlignment.h" #include "/usr/include/libMems/configuration.h" #include "/usr/include/libMems/dmSML/aPOSIXaio.h" #include "/usr/include/libMems/dmSML/alibc.h" #include "/usr/include/libMems/dmSML/alinuxaio.h" #include "/usr/include/libMems/dmSML/asyncio.h" #include "/usr/include/libMems/dmSML/awin32aio.h" #include "/usr/include/libMems/dmSML/buffer.h" #include "/usr/include/libMems/dmSML/dmsort.h" #include "/usr/include/libMems/dmSML/sml.h" #include "/usr/include/libMems/dmSML/sorting.h" #include "/usr/include/libMems/dmSML/timing.h" #include "/usr/include/libMems/dmSML/util.h" #include "/usr/include/libMems/gnAlignedSequences.h" #include "/usr/include/libMems/gnRAWSequence.h" #include "/usr/include/libMems/twister.h" // add namespaces namespace boost{typedef int tmp_add_type_1;} boost::tmp_add_type_1 tmp_add_func_1(){return 0;}; namespace boost{namespace algorithm{typedef int tmp_add_type_2;}} boost::algorithm::tmp_add_type_2 tmp_add_func_2(){return 0;}; namespace boost{namespace algorithm{namespace detail{typedef int tmp_add_type_3;}}} boost::algorithm::detail::tmp_add_type_3 tmp_add_func_3(){return 0;}; namespace boost{namespace concepts{typedef int tmp_add_type_4;}} boost::concepts::tmp_add_type_4 tmp_add_func_4(){return 0;}; namespace boost{namespace concepts{namespace detail{typedef int tmp_add_type_5;}}} boost::concepts::detail::tmp_add_type_5 tmp_add_func_5(){return 0;}; namespace boost{namespace core{typedef int tmp_add_type_6;}} boost::core::tmp_add_type_6 tmp_add_func_6(){return 0;}; namespace boost{namespace detail{typedef int tmp_add_type_7;}} boost::detail::tmp_add_type_7 tmp_add_func_7(){return 0;}; namespace boost{namespace detail{namespace function{typedef int tmp_add_type_8;}}} boost::detail::function::tmp_add_type_8 tmp_add_func_8(){return 0;}; namespace boost{namespace details{typedef int tmp_add_type_9;}} boost::details::tmp_add_type_9 tmp_add_func_9(){return 0;}; namespace boost{namespace details{namespace pool{typedef int tmp_add_type_10;}}} boost::details::pool::tmp_add_type_10 tmp_add_func_10(){return 0;}; namespace boost{namespace filesystem{typedef int tmp_add_type_11;}} boost::filesystem::tmp_add_type_11 tmp_add_func_11(){return 0;}; namespace boost{namespace filesystem{namespace detail{typedef int tmp_add_type_12;}}} boost::filesystem::detail::tmp_add_type_12 tmp_add_func_12(){return 0;}; namespace boost{namespace functional{typedef int tmp_add_type_13;}} boost::functional::tmp_add_type_13 tmp_add_func_13(){return 0;}; namespace boost{namespace functional{namespace detail{typedef int tmp_add_type_14;}}} boost::functional::detail::tmp_add_type_14 tmp_add_func_14(){return 0;}; namespace boost{namespace integer{typedef int tmp_add_type_15;}} boost::integer::tmp_add_type_15 tmp_add_func_15(){return 0;}; namespace boost{namespace integer{namespace detail{typedef int tmp_add_type_16;}}} boost::integer::detail::tmp_add_type_16 tmp_add_func_16(){return 0;}; namespace boost{namespace io{typedef int tmp_add_type_17;}} boost::io::tmp_add_type_17 tmp_add_func_17(){return 0;}; namespace boost{namespace io{namespace detail{typedef int tmp_add_type_18;}}} boost::io::detail::tmp_add_type_18 tmp_add_func_18(){return 0;}; namespace boost{namespace iostreams{typedef int tmp_add_type_19;}} boost::iostreams::tmp_add_type_19 tmp_add_func_19(){return 0;}; namespace boost{namespace iostreams{namespace detail{typedef int tmp_add_type_20;}}} boost::iostreams::detail::tmp_add_type_20 tmp_add_func_20(){return 0;}; namespace boost{namespace iterators{typedef int tmp_add_type_21;}} boost::iterators::tmp_add_type_21 tmp_add_func_21(){return 0;}; namespace boost{namespace iterators{namespace detail{typedef int tmp_add_type_22;}}} boost::iterators::detail::tmp_add_type_22 tmp_add_func_22(){return 0;}; namespace boost{namespace movelib{typedef int tmp_add_type_23;}} boost::movelib::tmp_add_type_23 tmp_add_func_23(){return 0;}; namespace boost{namespace movelib{namespace detail{typedef int tmp_add_type_24;}}} boost::movelib::detail::tmp_add_type_24 tmp_add_func_24(){return 0;}; namespace boost{namespace mpl{typedef int tmp_add_type_25;}} boost::mpl::tmp_add_type_25 tmp_add_func_25(){return 0;}; namespace boost{namespace mpl{namespace aux{typedef int tmp_add_type_26;}}} boost::mpl::aux::tmp_add_type_26 tmp_add_func_26(){return 0;}; namespace boost{namespace mpl{namespace placeholders{typedef int tmp_add_type_27;}}} boost::mpl::placeholders::tmp_add_type_27 tmp_add_func_27(){return 0;}; namespace boost{namespace range{typedef int tmp_add_type_28;}} boost::range::tmp_add_type_28 tmp_add_func_28(){return 0;}; namespace boost{namespace system{typedef int tmp_add_type_29;}} boost::system::tmp_add_type_29 tmp_add_func_29(){return 0;}; namespace boost{namespace system{namespace detail{typedef int tmp_add_type_30;}}} boost::system::detail::tmp_add_type_30 tmp_add_func_30(){return 0;}; namespace boost{namespace system{namespace errc{typedef int tmp_add_type_31;}}} boost::system::errc::tmp_add_type_31 tmp_add_func_31(){return 0;}; namespace boost{namespace typeindex{typedef int tmp_add_type_32;}} boost::typeindex::tmp_add_type_32 tmp_add_func_32(){return 0;}; namespace boost{namespace typeindex{namespace detail{typedef int tmp_add_type_33;}}} boost::typeindex::detail::tmp_add_type_33 tmp_add_func_33(){return 0;}; namespace genome{typedef int tmp_add_type_34;} genome::tmp_add_type_34 tmp_add_func_34(){return 0;}; namespace mems{typedef int tmp_add_type_35;} mems::tmp_add_type_35 tmp_add_func_35(){return 0;}; namespace boost{namespace __anon135ff9dda611{typedef int tmp_add_type_36;}} boost::__anon135ff9dda611::tmp_add_type_36 tmp_add_func_36(){return 0;}; namespace boost{namespace _mfi{typedef int tmp_add_type_37;}} boost::_mfi::tmp_add_type_37 tmp_add_func_37(){return 0;}; namespace boost{namespace binary_op_detail{typedef int tmp_add_type_38;}} boost::binary_op_detail::tmp_add_type_38 tmp_add_func_38(){return 0;}; namespace boost{namespace detail{namespace aligned_storage{typedef int tmp_add_type_39;}}} boost::detail::aligned_storage::tmp_add_type_39 tmp_add_func_39(){return 0;}; namespace boost{namespace detail{namespace dynamic_bitset_impl{typedef int tmp_add_type_40;}}} boost::detail::dynamic_bitset_impl::tmp_add_type_40 tmp_add_func_40(){return 0;}; namespace boost{namespace detail{namespace indirect_traits{typedef int tmp_add_type_41;}}} boost::detail::indirect_traits::tmp_add_type_41 tmp_add_func_41(){return 0;}; namespace boost{namespace detail{namespace multi_array{typedef int tmp_add_type_42;}}} boost::detail::multi_array::tmp_add_type_42 tmp_add_func_42(){return 0;}; namespace boost{namespace detail{namespace static_log2_impl{typedef int tmp_add_type_43;}}} boost::detail::static_log2_impl::tmp_add_type_43 tmp_add_func_43(){return 0;}; namespace boost{namespace empty_{typedef int tmp_add_type_44;}} boost::empty_::tmp_add_type_44 tmp_add_func_44(){return 0;}; namespace boost{namespace exception_detail{typedef int tmp_add_type_45;}} boost::exception_detail::tmp_add_type_45 tmp_add_func_45(){return 0;}; namespace boost{namespace filesystem{namespace path_detail{typedef int tmp_add_type_46;}}} boost::filesystem::path_detail::tmp_add_type_46 tmp_add_func_46(){return 0;}; namespace boost{namespace filesystem{namespace path_traits{typedef int tmp_add_type_47;}}} boost::filesystem::path_traits::tmp_add_type_47 tmp_add_func_47(){return 0;}; namespace boost{namespace hash_detail{typedef int tmp_add_type_48;}} boost::hash_detail::tmp_add_type_48 tmp_add_func_48(){return 0;}; namespace boost{namespace iostreams{namespace detail{namespace is_boost_stream_buffer_impl_{typedef int tmp_add_type_49;}}}} boost::iostreams::detail::is_boost_stream_buffer_impl_::tmp_add_type_49 tmp_add_func_49(){return 0;}; namespace boost{namespace iostreams{namespace detail{namespace is_boost_stream_impl_{typedef int tmp_add_type_50;}}}} boost::iostreams::detail::is_boost_stream_impl_::tmp_add_type_50 tmp_add_func_50(){return 0;}; namespace boost{namespace iostreams{namespace detail{namespace is_filtering_stream_impl_impl_{typedef int tmp_add_type_51;}}}} boost::iostreams::detail::is_filtering_stream_impl_impl_::tmp_add_type_51 tmp_add_func_51(){return 0;}; namespace boost{namespace iostreams{namespace detail{namespace is_filtering_streambuf_impl_impl_{typedef int tmp_add_type_52;}}}} boost::iostreams::detail::is_filtering_streambuf_impl_impl_::tmp_add_type_52 tmp_add_func_52(){return 0;}; namespace boost{namespace iostreams{namespace detail{namespace is_filtering_wstream_impl_impl_{typedef int tmp_add_type_53;}}}} boost::iostreams::detail::is_filtering_wstream_impl_impl_::tmp_add_type_53 tmp_add_func_53(){return 0;}; namespace boost{namespace iostreams{namespace detail{namespace is_filtering_wstreambuf_impl_impl_{typedef int tmp_add_type_54;}}}} boost::iostreams::detail::is_filtering_wstreambuf_impl_impl_::tmp_add_type_54 tmp_add_func_54(){return 0;}; namespace boost{namespace iostreams{namespace detail{namespace is_linked_impl_{typedef int tmp_add_type_55;}}}} boost::iostreams::detail::is_linked_impl_::tmp_add_type_55 tmp_add_func_55(){return 0;}; namespace boost{namespace iostreams{namespace is_filebuf_impl_{typedef int tmp_add_type_56;}}} boost::iostreams::is_filebuf_impl_::tmp_add_type_56 tmp_add_func_56(){return 0;}; namespace boost{namespace iostreams{namespace is_fstream_impl_{typedef int tmp_add_type_57;}}} boost::iostreams::is_fstream_impl_::tmp_add_type_57 tmp_add_func_57(){return 0;}; namespace boost{namespace iostreams{namespace is_ifstream_impl_{typedef int tmp_add_type_58;}}} boost::iostreams::is_ifstream_impl_::tmp_add_type_58 tmp_add_func_58(){return 0;}; namespace boost{namespace iostreams{namespace is_iostream_impl_{typedef int tmp_add_type_59;}}} boost::iostreams::is_iostream_impl_::tmp_add_type_59 tmp_add_func_59(){return 0;}; namespace boost{namespace iostreams{namespace is_istream_impl_{typedef int tmp_add_type_60;}}} boost::iostreams::is_istream_impl_::tmp_add_type_60 tmp_add_func_60(){return 0;}; namespace boost{namespace iostreams{namespace is_istringstream_impl_{typedef int tmp_add_type_61;}}} boost::iostreams::is_istringstream_impl_::tmp_add_type_61 tmp_add_func_61(){return 0;}; namespace boost{namespace iostreams{namespace is_iterator_range_impl_{typedef int tmp_add_type_62;}}} boost::iostreams::is_iterator_range_impl_::tmp_add_type_62 tmp_add_func_62(){return 0;}; namespace boost{namespace iostreams{namespace is_ofstream_impl_{typedef int tmp_add_type_63;}}} boost::iostreams::is_ofstream_impl_::tmp_add_type_63 tmp_add_func_63(){return 0;}; namespace boost{namespace iostreams{namespace is_ostream_impl_{typedef int tmp_add_type_64;}}} boost::iostreams::is_ostream_impl_::tmp_add_type_64 tmp_add_func_64(){return 0;}; namespace boost{namespace iostreams{namespace is_ostringstream_impl_{typedef int tmp_add_type_65;}}} boost::iostreams::is_ostringstream_impl_::tmp_add_type_65 tmp_add_func_65(){return 0;}; namespace boost{namespace iostreams{namespace is_streambuf_impl_{typedef int tmp_add_type_66;}}} boost::iostreams::is_streambuf_impl_::tmp_add_type_66 tmp_add_func_66(){return 0;}; namespace boost{namespace iostreams{namespace is_stringbuf_impl_{typedef int tmp_add_type_67;}}} boost::iostreams::is_stringbuf_impl_::tmp_add_type_67 tmp_add_func_67(){return 0;}; namespace boost{namespace iostreams{namespace is_stringstream_impl_{typedef int tmp_add_type_68;}}} boost::iostreams::is_stringstream_impl_::tmp_add_type_68 tmp_add_func_68(){return 0;}; namespace boost{namespace iterator_range_detail{typedef int tmp_add_type_69;}} boost::iterator_range_detail::tmp_add_type_69 tmp_add_func_69(){return 0;}; namespace boost{namespace iterators{namespace advance_adl_barrier{typedef int tmp_add_type_70;}}} boost::iterators::advance_adl_barrier::tmp_add_type_70 tmp_add_func_70(){return 0;}; namespace boost{namespace iterators{namespace distance_adl_barrier{typedef int tmp_add_type_71;}}} boost::iterators::distance_adl_barrier::tmp_add_type_71 tmp_add_func_71(){return 0;}; namespace boost{namespace move_detail{typedef int tmp_add_type_72;}} boost::move_detail::tmp_add_type_72 tmp_add_func_72(){return 0;}; namespace boost{namespace multi_array_concepts{typedef int tmp_add_type_73;}} boost::multi_array_concepts::tmp_add_type_73 tmp_add_func_73(){return 0;}; namespace boost{namespace multi_array_concepts{namespace detail{typedef int tmp_add_type_74;}}} boost::multi_array_concepts::detail::tmp_add_type_74 tmp_add_func_74(){return 0;}; namespace boost{namespace multi_array_types{typedef int tmp_add_type_75;}} boost::multi_array_types::tmp_add_type_75 tmp_add_func_75(){return 0;}; namespace boost{namespace next_prior_detail{typedef int tmp_add_type_76;}} boost::next_prior_detail::tmp_add_type_76 tmp_add_func_76(){return 0;}; namespace boost{namespace noncopyable_{typedef int tmp_add_type_77;}} boost::noncopyable_::tmp_add_type_77 tmp_add_func_77(){return 0;}; namespace boost{namespace range_adl_barrier{typedef int tmp_add_type_78;}} boost::range_adl_barrier::tmp_add_type_78 tmp_add_func_78(){return 0;}; namespace boost{namespace range_detail{typedef int tmp_add_type_79;}} boost::range_detail::tmp_add_type_79 tmp_add_func_79(){return 0;}; namespace boost{namespace range_distance_adl_barrier{typedef int tmp_add_type_80;}} boost::range_distance_adl_barrier::tmp_add_type_80 tmp_add_func_80(){return 0;}; namespace boost{namespace sp_adl_block{typedef int tmp_add_type_81;}} boost::sp_adl_block::tmp_add_type_81 tmp_add_func_81(){return 0;}; namespace boost{namespace tt_align_ns{typedef int tmp_add_type_82;}} boost::tt_align_ns::tmp_add_type_82 tmp_add_func_82(){return 0;}; namespace boost{namespace type_traits{typedef int tmp_add_type_83;}} boost::type_traits::tmp_add_type_83 tmp_add_func_83(){return 0;}; namespace boost{namespace type_traits{namespace detail{typedef int tmp_add_type_84;}}} boost::type_traits::detail::tmp_add_type_84 tmp_add_func_84(){return 0;}; namespace boost{namespace type_traits_detail{typedef int tmp_add_type_85;}} boost::type_traits_detail::tmp_add_type_85 tmp_add_func_85(){return 0;}; namespace boost{namespace type_traits_swappable_detail{typedef int tmp_add_type_86;}} boost::type_traits_swappable_detail::tmp_add_type_86 tmp_add_func_86(){return 0;}; namespace boost_concepts{typedef int tmp_add_type_87;} boost_concepts::tmp_add_type_87 tmp_add_func_87(){return 0;}; namespace boost_concepts{namespace detail{typedef int tmp_add_type_88;}} boost_concepts::detail::tmp_add_type_88 tmp_add_func_88(){return 0;}; namespace boost_swap_impl{typedef int tmp_add_type_89;} boost_swap_impl::tmp_add_type_89 tmp_add_func_89(){return 0;}; namespace mpl_{typedef int tmp_add_type_90;} mpl_::tmp_add_type_90 tmp_add_func_90(){return 0;}; namespace mpl_{namespace aux{typedef int tmp_add_type_91;}} mpl_::aux::tmp_add_type_91 tmp_add_func_91(){return 0;}; // add classes BFloat* tmp_add_class_0; BFloatMethods* tmp_add_class_1; HomologyBaumWelch* tmp_add_class_2; HomologyDPTable* tmp_add_class_3; Logspace* tmp_add_class_4; LogspaceMethods* tmp_add_class_5; Params* tmp_add_class_6; Path* tmp_add_class_7; SMLHeader_s* tmp_add_class_8; SimplePath* tmp_add_class_9; TreeNode* tmp_add_class_10; _BFloatInitialize* tmp_add_class_11; _G_fpos64_t* tmp_add_class_12; _G_fpos_t* tmp_add_class_13; _IO_cookie_io_functions_t* tmp_add_class_14; _aFILE* tmp_add_class_15; _aIORec* tmp_add_class_16; bin_s* tmp_add_class_17; buffer_list_s* tmp_add_class_18; buffer_s* tmp_add_class_19; device_s* tmp_add_class_20; iodevice_s* tmp_add_class_21; record_s* tmp_add_class_22; seqbuf_s* tmp_add_class_23; sml_s* tmp_add_class_24; sort_buf_s* tmp_add_class_25; working_set_s* tmp_add_class_26; The GCC parameters: gcc -fdump-lang-raw -fkeep-inline-functions -c -x c++ -fpermissive -w "/tmp/NyLyVFOGg0/dump1.h" In file included from /tmp/NyLyVFOGg0/dump1.h:12: /usr/include/libMems/AbstractGappedAlignment.h:80:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’? 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^~~~~~~~~~ | gnContigSequence /usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 1 is invalid 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^ /usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 2 is invalid /usr/include/libMems/AbstractGappedAlignment.h:80:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’? 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^~~~~~~~~~ | gnContigSequence /usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 1 is invalid 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^ /usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 2 is invalid /usr/include/libMems/AbstractGappedAlignment.h:80:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’? 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^~~~~~~~~~ | gnContigSequence /usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 1 is invalid 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^ /usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 2 is invalid /usr/include/libMems/AbstractGappedAlignment.h:80:51: error: invalid template-id 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^~~ /usr/include/libMems/AbstractGappedAlignment.h:80:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’? 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^~~~~~~~~~ | gnContigSequence /usr/include/libMems/AbstractGappedAlignment.h:80:84: error: expected primary-expression before ‘>’ token 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^ /usr/include/libMems/AbstractGappedAlignment.h:80:45: error: template placeholder type ‘const vector<...auto...>’ must be followed by a simple declarator-id 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^~~~~ In file included from /usr/include/c++/12/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/AbstractGappedAlignment.h:16: /usr/include/c++/12/bits/stl_vector.h:423:11: note: ‘template class std::vector’ declared here 423 | class vector : protected _Vector_base<_Tp, _Alloc> | ^~~~~~ /usr/include/libMems/AbstractGappedAlignment.h:80:96: error: expected ‘)’ before ‘,’ token 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ~ ^ | ) /usr/include/libMems/AbstractGappedAlignment.h:80:122: error: invalid declarator before ‘&’ token 80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ); | ^ /usr/include/libMems/AbstractGappedAlignment.h:84:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’? 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^~~~~~~~~~ | gnContigSequence /usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 1 is invalid 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^ /usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 2 is invalid /usr/include/libMems/AbstractGappedAlignment.h:84:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’? 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^~~~~~~~~~ | gnContigSequence /usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 1 is invalid 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^ /usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 2 is invalid /usr/include/libMems/AbstractGappedAlignment.h:84:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’? 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^~~~~~~~~~ | gnContigSequence /usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 1 is invalid 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^ /usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 2 is invalid /usr/include/libMems/AbstractGappedAlignment.h:84:51: error: invalid template-id 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^~~ /usr/include/libMems/AbstractGappedAlignment.h:84:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’? 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^~~~~~~~~~ | gnContigSequence /usr/include/libMems/AbstractGappedAlignment.h:84:84: error: expected primary-expression before ‘>’ token 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^ /usr/include/libMems/AbstractGappedAlignment.h:84:45: error: template placeholder type ‘const vector<...auto...>’ must be followed by a simple declarator-id 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^~~~~ /usr/include/c++/12/bits/stl_vector.h:423:11: note: ‘template class std::vector’ declared here 423 | class vector : protected _Vector_base<_Tp, _Alloc> | ^~~~~~ /usr/include/libMems/AbstractGappedAlignment.h:84:96: error: expected ‘)’ before ‘,’ token 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ~ ^ | ) /usr/include/libMems/AbstractGappedAlignment.h:84:122: error: invalid declarator before ‘&’ token 84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector& alignment ) | ^ In file included from /tmp/NyLyVFOGg0/dump1.h:20: /usr/include/libMems/DistanceMatrix.h: In instantiation of ‘void mems::AddToMatchIdentityMatrix(const AbstractMatchType&, const std::vector&, NumericMatrix&) [with AbstractMatchType = AbstractMatch]’: /usr/include/libMems/DistanceMatrix.h:60:27: required from ‘void mems::IdentityMatrix(const AbstractMatchVectorType&, const std::vector&, NumericMatrix&) [with AbstractMatchVectorType = std::vector]’ /usr/include/libMems/DistanceMatrix.h:45:16: required from here /usr/include/libMems/DistanceMatrix.h:164:21: error: cannot allocate an object of abstract type ‘mems::AbstractMatch’ 164 | GetAlignment( amt, seq_table, alignment ); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/libMems/AbstractMatch.h:88:7: note: because the following virtual functions are pure within ‘mems::AbstractMatch’: 88 | class AbstractMatch : public genome::gnClone { | ^~~~~~~~~~~~~ In file included from /usr/include/libMems/AbstractMatch.h:16: /usr/include/libGenome/gnClone.h:28:34: note: ‘virtual genome::gnClone* genome::gnClone::Clone() const’ 28 | virtual gnClone* Clone() const = 0; | ^~~~~ /usr/include/libMems/AbstractMatch.h:98:32: note: ‘virtual mems::AbstractMatch* mems::AbstractMatch::Copy() const’ 98 | virtual AbstractMatch* Copy() const = 0; | ^~~~ /usr/include/libMems/AbstractMatch.h:101:22: note: ‘virtual void mems::AbstractMatch::Free()’ 101 | virtual void Free() = 0; | ^~~~ /usr/include/libMems/AbstractMatch.h:104:24: note: ‘virtual gnSeqI mems::AbstractMatch::Length(uint) const’ 104 | virtual gnSeqI Length( uint seqI ) const = 0; | ^~~~~~ /usr/include/libMems/AbstractMatch.h:107:22: note: ‘virtual void mems::AbstractMatch::SetLength(gnSeqI, uint)’ 107 | virtual void SetLength( gnSeqI len, uint seqI ) = 0; | ^~~~~~~~~ /usr/include/libMems/AbstractMatch.h:111:23: note: ‘virtual int64 mems::AbstractMatch::Start(uint) const’ 111 | virtual int64 Start(uint startI) const = 0; | ^~~~~ /usr/include/libMems/AbstractMatch.h:115:22: note: ‘virtual void mems::AbstractMatch::SetStart(uint, int64)’ 115 | virtual void SetStart(uint seqI, int64 start) = 0; | ^~~~~~~~ /usr/include/libMems/AbstractMatch.h:126:24: note: ‘virtual gnSeqI mems::AbstractMatch::LeftEnd(uint) const’ 126 | virtual gnSeqI LeftEnd(uint seqI) const = 0; | ^~~~~~~ /usr/include/libMems/AbstractMatch.h:135:29: note: ‘virtual mems::AbstractMatch::orientation mems::AbstractMatch::Orientation(uint) const’ 135 | virtual orientation Orientation(uint seqI) const = 0; | ^~~~~~~~~~~ /usr/include/libMems/AbstractMatch.h:138:22: note: ‘virtual void mems::AbstractMatch::SetLeftEnd(uint, gnSeqI)’ 138 | virtual void SetLeftEnd(uint seqI, gnSeqI start) = 0; | ^~~~~~~~~~ /usr/include/libMems/AbstractMatch.h:141:22: note: ‘virtual void mems::AbstractMatch::SetOrientation(uint, orientation)’ 141 | virtual void SetOrientation(uint seqI, orientation o) = 0; | ^~~~~~~~~~~~~~ /usr/include/libMems/AbstractMatch.h:144:22: note: ‘virtual void mems::AbstractMatch::MoveStart(int64)’ 144 | virtual void MoveStart(int64 move_amount) = 0; | ^~~~~~~~~ /usr/include/libMems/AbstractMatch.h:146:22: note: ‘virtual void mems::AbstractMatch::MoveEnd(int64)’ 146 | virtual void MoveEnd(int64 move_amount) = 0; | ^~~~~~~ /usr/include/libMems/AbstractMatch.h:149:22: note: ‘virtual uint mems::AbstractMatch::Multiplicity() const’ 149 | virtual uint Multiplicity() const = 0; | ^~~~~~~~~~~~ /usr/include/libMems/AbstractMatch.h:152:22: note: ‘virtual uint mems::AbstractMatch::SeqCount() const’ 152 | virtual uint SeqCount() const = 0; | ^~~~~~~~ /usr/include/libMems/AbstractMatch.h:155:22: note: ‘virtual uint mems::AbstractMatch::FirstStart() const’ 155 | virtual uint FirstStart() const = 0; | ^~~~~~~~~~ /usr/include/libMems/AbstractMatch.h:158:24: note: ‘virtual gnSeqI mems::AbstractMatch::AlignmentLength() const’ 158 | virtual gnSeqI AlignmentLength() const = 0; | ^~~~~~~~~~~~~~~ /usr/include/libMems/AbstractMatch.h:161:22: note: ‘virtual void mems::AbstractMatch::Invert()’ 161 | virtual void Invert() = 0; | ^~~~~~ /usr/include/libMems/AbstractMatch.h:168:22: note: ‘virtual void mems::AbstractMatch::CropStart(gnSeqI)’ 168 | virtual void CropStart(gnSeqI crop_amount) = 0; | ^~~~~~~~~ /usr/include/libMems/AbstractMatch.h:173:22: note: ‘virtual void mems::AbstractMatch::CropEnd(gnSeqI)’ 173 | virtual void CropEnd(gnSeqI crop_amount) = 0; | ^~~~~~~ /usr/include/libMems/AbstractMatch.h:179:22: note: ‘virtual void mems::AbstractMatch::CropLeft(gnSeqI, uint)’ 179 | virtual void CropLeft(gnSeqI crop_amount, uint seqI) = 0; | ^~~~~~~~ /usr/include/libMems/AbstractMatch.h:184:22: note: ‘virtual void mems::AbstractMatch::CropRight(gnSeqI, uint)’ 184 | virtual void CropRight(gnSeqI crop_amount, uint seqI) = 0; | ^~~~~~~~~ /usr/include/libMems/AbstractMatch.h:191:22: note: ‘virtual void mems::AbstractMatch::GetAlignment(std::vector >&) const’ 191 | virtual void GetAlignment( std::vector< bitset_t >& align_matrix ) const = 0; | ^~~~~~~~~~~~ /usr/include/libMems/AbstractMatch.h:200:22: note: ‘virtual void mems::AbstractMatch::GetColumn(gnSeqI, std::vector&, std::vector&) const’ 200 | virtual void GetColumn( gnSeqI col, std::vector& pos, std::vector& column ) const = 0; | ^~~~~~~~~ /usr/include/libMems/AbstractMatch.h:204:22: note: ‘virtual bool mems::AbstractMatch::IsGap(uint, gnSeqI) const’ 204 | virtual bool IsGap( uint seq, gnSeqI col ) const = 0; | ^~~~~ /usr/include/libMems/AbstractMatch.h:206:22: note: ‘virtual uint mems::AbstractMatch::UsedSeq(uint) const’ 206 | virtual uint UsedSeq( uint seqI ) const = 0; | ^~~~~~~