Temporary header file '/tmp/JqzTsoYymA/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/lib/gcc/arm-linux-gnueabihf/12/include/stddef.h" #include "/usr/include/libGenome/IntervalSequenceTree.h" #include "/usr/include/libGenome/OmpGuard.h" #include "/usr/include/libGenome/gnABISource.h" #include "/usr/include/libGenome/gnBaseFeature.h" #include "/usr/include/libGenome/gnBaseFilter.h" #include "/usr/include/libGenome/gnBaseHeader.h" #include "/usr/include/libGenome/gnBaseQualifier.h" #include "/usr/include/libGenome/gnBaseSource.h" #include "/usr/include/libGenome/gnBaseSpec.h" #include "/usr/include/libGenome/gnClone.h" #include "/usr/include/libGenome/gnCompare.h" #include "/usr/include/libGenome/gnContigSpec.h" #include "/usr/include/libGenome/gnDNASequence.h" #include "/usr/include/libGenome/gnDataBaseSource.h" #include "/usr/include/libGenome/gnDebug.h" #include "/usr/include/libGenome/gnDefs.h" #include "/usr/include/libGenome/gnException.h" #include "/usr/include/libGenome/gnExceptionCode.h" #include "/usr/include/libGenome/gnFASSource.h" #include "/usr/include/libGenome/gnFastTranslator.h" #include "/usr/include/libGenome/gnFeature.h" #include "/usr/include/libGenome/gnFileContig.h" #include "/usr/include/libGenome/gnFileSource.h" #include "/usr/include/libGenome/gnFilter.h" #include "/usr/include/libGenome/gnFragmentSpec.h" #include "/usr/include/libGenome/gnGBKSource.h" #include "/usr/include/libGenome/gnGenomeSpec.h" #include "/usr/include/libGenome/gnLocation.h" #include "/usr/include/libGenome/gnMultiSpec.h" #include "/usr/include/libGenome/gnPosSpecificTranslator.h" #include "/usr/include/libGenome/gnProteinSequence.h" #include "/usr/include/libGenome/gnRAWSource.h" #include "/usr/include/libGenome/gnRNASequence.h" #include "/usr/include/libGenome/gnSEQSource.h" #include "/usr/include/libGenome/gnSequence.h" #include "/usr/include/libGenome/gnSetup.h" #include "/usr/include/libGenome/gnSourceFactory.h" #include "/usr/include/libGenome/gnSourceHeader.h" #include "/usr/include/libGenome/gnSourceQualifier.h" #include "/usr/include/libGenome/gnSourceSpec.h" #include "/usr/include/libGenome/gnStringHeader.h" #include "/usr/include/libGenome/gnStringQualifier.h" #include "/usr/include/libGenome/gnStringSpec.h" #include "/usr/include/libGenome/gnStringTools.h" #include "/usr/include/libGenome/gnTranslator.h" #include "/usr/include/libGenome/gnVersion.h" // add namespaces namespace genome{typedef int tmp_add_type_1;} genome::tmp_add_type_1 tmp_add_func_1(){return 0;}; // add classes _G_fpos64_t* tmp_add_class_0; _G_fpos_t* tmp_add_class_1; _IO_cookie_io_functions_t* tmp_add_class_2; The GCC parameters: gcc -fdump-lang-raw -fkeep-inline-functions -c -x c++ -fpermissive -w "/tmp/JqzTsoYymA/dump1.h" In file included from /tmp/JqzTsoYymA/dump1.h:13: /usr/include/libGenome/IntervalSequenceTree.h:29:14: error: ‘uint64’ does not name a type 29 | static const uint64 IST_END = ((0xFFFFFFFF << 31) << 1 ) + 0xFFFFFFFF; | ^~~~~~ /usr/include/libGenome/IntervalSequenceTree.h:179:58: error: ‘int64’ has not been declared 179 | static void propogateChanges( IstNode* cur_node, int64 length_diff, int64 subtree_diff ); | ^~~~~ /usr/include/libGenome/IntervalSequenceTree.h:179:77: error: ‘int64’ has not been declared 179 | static void propogateChanges( IstNode* cur_node, int64 length_diff, int64 subtree_diff ); | ^~~~~ /usr/include/libGenome/IntervalSequenceTree.h:155:67: error: ‘IST_END’ was not declared in this scope 155 | iterator insert( const value_type& val, size_type point = IST_END ); | ^~~~~~~ /usr/include/libGenome/IntervalSequenceTree.h:157:80: error: ‘IST_END’ was not declared in this scope 157 | void insert(InputIterator first, InputIterator last, size_type point = IST_END ); | ^~~~~~~ /usr/include/libGenome/IntervalSequenceTree.h: In member function ‘IntervalSequenceTree::size_type IntervalSequenceTree::max_size() const’: /usr/include/libGenome/IntervalSequenceTree.h:273:16: error: ‘IST_END’ was not declared in this scope 273 | return IST_END - 1; | ^~~~~~~ /usr/include/libGenome/IntervalSequenceTree.h: In static member function ‘static void IntervalSequenceTree::checkTree(node_pointer)’: /usr/include/libGenome/IntervalSequenceTree.h:287:30: error: ‘cerr’ is not a member of ‘std’ 287 | std::cerr << "freakout\n"; | ^~~~ /usr/include/libGenome/IntervalSequenceTree.h:5:1: note: ‘std::cerr’ is defined in header ‘’; did you forget to ‘#include ’? 4 | #include +++ |+#include 5 | /usr/include/libGenome/IntervalSequenceTree.h: At global scope: /usr/include/libGenome/IntervalSequenceTree.h:524:9: error: ‘int64’ has not been declared 524 | int64 length_diff, | ^~~~~ /usr/include/libGenome/IntervalSequenceTree.h:525:9: error: ‘int64’ has not been declared 525 | int64 subtree_diff ) | ^~~~~ /usr/include/libGenome/IntervalSequenceTree.h: In static member function ‘static void IntervalSequenceTree::propogateChanges(IstNode*, int, int)’: /usr/include/libGenome/IntervalSequenceTree.h:530:30: error: ‘cerr’ is not a member of ‘std’ 530 | std::cerr << "when I say oh, you say shit!"; | ^~~~ /usr/include/libGenome/IntervalSequenceTree.h:530:30: note: ‘std::cerr’ is defined in header ‘’; did you forget to ‘#include ’? In file included from /tmp/JqzTsoYymA/dump1.h:25: /usr/include/libGenome/gnDNASequence.h: At global scope: /usr/include/libGenome/gnDNASequence.h:79:9: error: ‘list’ does not name a type 79 | list filter_list; | ^~~~ /usr/include/libGenome/gnDNASequence.h: In constructor ‘genome::gnDNASequence::gnDNASequence()’: /usr/include/libGenome/gnDNASequence.h:85:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 85 | filter_list.push_back(gnFilter::fullDNASeqFilter()); | ^~~~~~~~~~~ In file included from /usr/include/libGenome/gnABISource.h:22, from /tmp/JqzTsoYymA/dump1.h:15: /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnDNASequence.h: In constructor ‘genome::gnDNASequence::gnDNASequence(const gnSeqC*)’: /usr/include/libGenome/gnDNASequence.h:90:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 90 | filter_list.push_back(gnFilter::fullDNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnDNASequence.h: In constructor ‘genome::gnDNASequence::gnDNASequence(const std::string&)’: /usr/include/libGenome/gnDNASequence.h:95:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 95 | filter_list.push_back(gnFilter::fullDNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnDNASequence.h: In constructor ‘genome::gnDNASequence::gnDNASequence(const genome::gnGenomeSpec&)’: /usr/include/libGenome/gnDNASequence.h:100:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 100 | filter_list.push_back(gnFilter::fullDNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnDNASequence.h: In constructor ‘genome::gnDNASequence::gnDNASequence(const genome::gnFragmentSpec&)’: /usr/include/libGenome/gnDNASequence.h:105:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 105 | filter_list.push_back(gnFilter::fullDNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnDNASequence.h: In constructor ‘genome::gnDNASequence::gnDNASequence(const genome::gnContigSpec&)’: /usr/include/libGenome/gnDNASequence.h:110:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 110 | filter_list.push_back(gnFilter::fullDNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnDNASequence.h: In constructor ‘genome::gnDNASequence::gnDNASequence(gnSeqC*, gnSeqI)’: /usr/include/libGenome/gnDNASequence.h:115:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 115 | filter_list.push_back(gnFilter::fullDNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnDNASequence.h: In copy constructor ‘genome::gnDNASequence::gnDNASequence(const genome::gnDNASequence&)’: /usr/include/libGenome/gnDNASequence.h:120:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 120 | filter_list.push_back(gnFilter::fullDNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ In file included from /tmp/JqzTsoYymA/dump1.h:26: /usr/include/libGenome/gnDataBaseSource.h: At global scope: /usr/include/libGenome/gnDataBaseSource.h:33:35: error: expected class-name before ‘(’ token 33 | virtual ~gnDataBaseSourcee(){} | ^ /usr/include/libGenome/gnDataBaseSource.h:37:31: error: ‘virtual genome::gnBaseSource* genome::gnDataBaseSource::Clone() const’ cannot be overloaded with ‘virtual genome::gnDataBaseSource* genome::gnDataBaseSource::Clone() const’ 37 | virtual gnBaseSource* Clone() const = 0; | ^~~~~ /usr/include/libGenome/gnDataBaseSource.h:35:35: note: previous declaration ‘virtual genome::gnDataBaseSource* genome::gnDataBaseSource::Clone() const’ 35 | virtual gnDataBaseSource* Clone() const = 0; | ^~~~~ /usr/include/libGenome/gnDataBaseSource.h:39:25: error: conflicting return type specified for ‘virtual boolean genome::gnDataBaseSource::Open(std::string)’ 39 | virtual boolean Open( std::string openString ) = 0; | ^~~~ In file included from /usr/include/libGenome/gnSequence.h:26: /usr/include/libGenome/gnBaseSource.h:56:22: note: overridden function is ‘virtual void genome::gnBaseSource::Open(std::string)’ 56 | virtual void Open( std::string openString ) = 0; | ^~~~ /usr/include/libGenome/gnDataBaseSource.h:40:25: error: conflicting return type specified for ‘virtual boolean genome::gnDataBaseSource::Open()’ 40 | virtual boolean Open() = 0; | ^~~~ /usr/include/libGenome/gnBaseSource.h:62:22: note: overridden function is ‘virtual void genome::gnBaseSource::Open()’ 62 | virtual void Open() = 0; | ^~~~ /usr/include/libGenome/gnDataBaseSource.h:41:25: error: conflicting return type specified for ‘virtual boolean genome::gnDataBaseSource::Close()’ 41 | virtual boolean Close() = 0; | ^~~~~ /usr/include/libGenome/gnBaseSource.h:67:22: note: overridden function is ‘virtual void genome::gnBaseSource::Close()’ 67 | virtual void Close() = 0; | ^~~~~ /usr/include/libGenome/gnDataBaseSource.h:49:25: error: conflicting return type specified for ‘virtual boolean genome::gnDataBaseSource::SetFilter(genome::gnFilter*)’ 49 | virtual boolean SetFilter( gnFilter* filter ) = 0; | ^~~~~~~~~ /usr/include/libGenome/gnBaseSource.h:119:22: note: overridden function is ‘virtual void genome::gnBaseSource::SetFilter(genome::gnFilter*)’ 119 | virtual void SetFilter( gnFilter* filter ) = 0; | ^~~~~~~~~ In file included from /tmp/JqzTsoYymA/dump1.h:43: /usr/include/libGenome/gnProteinSequence.h:80:9: error: ‘list’ does not name a type 80 | list filter_list; | ^~~~ /usr/include/libGenome/gnProteinSequence.h: In constructor ‘genome::gnProteinSequence::gnProteinSequence()’: /usr/include/libGenome/gnProteinSequence.h:86:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 86 | filter_list.push_back(gnFilter::proteinSeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnProteinSequence.h: In constructor ‘genome::gnProteinSequence::gnProteinSequence(const gnSeqC*)’: /usr/include/libGenome/gnProteinSequence.h:91:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 91 | filter_list.push_back(gnFilter::proteinSeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnProteinSequence.h: In constructor ‘genome::gnProteinSequence::gnProteinSequence(const std::string&)’: /usr/include/libGenome/gnProteinSequence.h:96:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 96 | filter_list.push_back(gnFilter::proteinSeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnProteinSequence.h: In constructor ‘genome::gnProteinSequence::gnProteinSequence(const genome::gnGenomeSpec&)’: /usr/include/libGenome/gnProteinSequence.h:101:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 101 | filter_list.push_back(gnFilter::proteinSeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnProteinSequence.h: In constructor ‘genome::gnProteinSequence::gnProteinSequence(const genome::gnFragmentSpec&)’: /usr/include/libGenome/gnProteinSequence.h:106:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 106 | filter_list.push_back(gnFilter::proteinSeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnProteinSequence.h: In constructor ‘genome::gnProteinSequence::gnProteinSequence(const genome::gnContigSpec&)’: /usr/include/libGenome/gnProteinSequence.h:111:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 111 | filter_list.push_back(gnFilter::proteinSeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnProteinSequence.h: In constructor ‘genome::gnProteinSequence::gnProteinSequence(gnSeqC*, gnSeqI)’: /usr/include/libGenome/gnProteinSequence.h:116:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 116 | filter_list.push_back(gnFilter::proteinSeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnProteinSequence.h: In copy constructor ‘genome::gnProteinSequence::gnProteinSequence(const genome::gnProteinSequence&)’: /usr/include/libGenome/gnProteinSequence.h:121:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 121 | filter_list.push_back(gnFilter::proteinSeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ In file included from /tmp/JqzTsoYymA/dump1.h:45: /usr/include/libGenome/gnRNASequence.h: At global scope: /usr/include/libGenome/gnRNASequence.h:80:9: error: ‘list’ does not name a type 80 | list filter_list; | ^~~~ /usr/include/libGenome/gnRNASequence.h: In constructor ‘genome::gnRNASequence::gnRNASequence()’: /usr/include/libGenome/gnRNASequence.h:86:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 86 | filter_list.push_back(gnFilter::fullRNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnRNASequence.h: In constructor ‘genome::gnRNASequence::gnRNASequence(const gnSeqC*)’: /usr/include/libGenome/gnRNASequence.h:91:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 91 | filter_list.push_back(gnFilter::fullRNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnRNASequence.h: In constructor ‘genome::gnRNASequence::gnRNASequence(const std::string&)’: /usr/include/libGenome/gnRNASequence.h:96:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 96 | filter_list.push_back(gnFilter::fullRNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnRNASequence.h: In constructor ‘genome::gnRNASequence::gnRNASequence(const genome::gnGenomeSpec&)’: /usr/include/libGenome/gnRNASequence.h:101:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 101 | filter_list.push_back(gnFilter::fullRNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnRNASequence.h: In constructor ‘genome::gnRNASequence::gnRNASequence(const genome::gnFragmentSpec&)’: /usr/include/libGenome/gnRNASequence.h:106:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 106 | filter_list.push_back(gnFilter::fullRNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnRNASequence.h: In constructor ‘genome::gnRNASequence::gnRNASequence(const genome::gnContigSpec&)’: /usr/include/libGenome/gnRNASequence.h:111:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 111 | filter_list.push_back(gnFilter::fullRNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnRNASequence.h: In constructor ‘genome::gnRNASequence::gnRNASequence(gnSeqC*, gnSeqI)’: /usr/include/libGenome/gnRNASequence.h:116:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 116 | filter_list.push_back(gnFilter::fullRNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~ /usr/include/libGenome/gnRNASequence.h: In copy constructor ‘genome::gnRNASequence::gnRNASequence(const genome::gnRNASequence&)’: /usr/include/libGenome/gnRNASequence.h:121:9: error: ‘std::__cxx11::list genome::gnSequence::filter_list’ is private within this context 121 | filter_list.push_back(gnFilter::fullRNASeqFilter()); | ^~~~~~~~~~~ /usr/include/libGenome/gnSequence.h:511:40: note: declared private here 511 | std::list filter_list; | ^~~~~~~~~~~