Temporary header file '/tmp/82Zk4_TBrb/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/clustalo/clustal/hhalign_wrapper.h" #include "/usr/include/clustalo/clustal/ktuple_pair.h" #include "/usr/include/clustalo/clustal/log.h" #include "/usr/include/clustalo/clustal/mbed.h" #include "/usr/include/clustalo/clustal/muscle_tree.h" #include "/usr/include/clustalo/clustal/pair_dist.h" #include "/usr/include/clustalo/clustal/progress.h" #include "/usr/include/clustalo/clustal/seq.h" #include "/usr/include/clustalo/clustal/symmatrix.h" #include "/usr/include/clustalo/clustal/tree.h" #include "/usr/include/clustalo/clustal/util.h" #include "/usr/include/clustalo/clustal/weights.h" #include "/usr/include/clustalo/clustal-omega-config.h" #include "/usr/include/clustalo/clustal-omega.h" #include "/usr/include/clustalo/hhalign/general.h" #include "/usr/include/clustalo/hhalign/hhfunc.h" #include "/usr/include/clustalo/squid/gki.h" #include "/usr/include/clustalo/squid/gsi64.h" #include "/usr/include/clustalo/squid/msa.h" #include "/usr/include/clustalo/squid/rk.h" #include "/usr/include/clustalo/squid/sqfuncs.h" #include "/usr/include/clustalo/squid/squid.h" #include "/usr/include/clustalo/squid/sre_random.h" #include "/usr/include/clustalo/squid/ssi.h" #include "/usr/include/clustalo/squid/stockholm.h" #include "/usr/include/clustalo/squid/stopwatch.h" #include "/usr/include/clustalo/squid/vectorops.h" #include "/usr/include/clustalo/squid/version.h" // add classes ReadSeqVars* tmp_add_class_0; _G_fpos64_t* tmp_add_class_1; _G_fpos_t* tmp_add_class_2; _IO_cookie_io_functions_t* tmp_add_class_3; aliinfo_s* tmp_add_class_4; gki_elem* tmp_add_class_5; intstack_s* tmp_add_class_6; iupactype* tmp_add_class_7; msa_struct* tmp_add_class_8; msafile_struct* tmp_add_class_9; opt_s* tmp_add_class_10; phylo_s* tmp_add_class_11; seqinfo_s* tmp_add_class_12; sqd_regexp* tmp_add_class_13; ssifile_s* tmp_add_class_14; ssiindex_s* tmp_add_class_15; ssioffset_s* tmp_add_class_16; ssipkey_s* tmp_add_class_17; ssiskey_s* tmp_add_class_18; stopwatch_s* tmp_add_class_19; tms* tmp_add_class_20; The GCC parameters: gcc -fdump-lang-raw -fkeep-inline-functions -c -x c++ -fpermissive -w "/tmp/82Zk4_TBrb/dump1.h" -I/usr/include/clustalo In file included from /tmp/82Zk4_TBrb/dump1.h:12: /usr/include/clustalo/clustal/hhalign_wrapper.h:20:1: error: variable or field ‘SetDefaultHhalignPara’ declared void 20 | SetDefaultHhalignPara(hhalign_para *prHhalignPara); | ^~~~~~~~~~~~~~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:20:23: error: ‘hhalign_para’ was not declared in this scope 20 | SetDefaultHhalignPara(hhalign_para *prHhalignPara); | ^~~~~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:20:37: error: ‘prHhalignPara’ was not declared in this scope 20 | SetDefaultHhalignPara(hhalign_para *prHhalignPara); | ^~~~~~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:23:24: error: ‘mseq_t’ was not declared in this scope 23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile); | ^~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:23:32: error: ‘prMSeq’ was not declared in this scope 23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile); | ^~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:23:40: error: ‘hmm_light’ was not declared in this scope 23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile); | ^~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:23:65: error: ‘hhalign_para’ was not declared in this scope 23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile); | ^~~~~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:23:92: error: expected primary-expression before ‘char’ 23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile); | ^~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:26:8: error: ‘mseq_t’ was not declared in this scope 26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize); | ^~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:26:16: error: ‘prMSeq’ was not declared in this scope 26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize); | ^~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:26:24: error: ‘hhalign_para’ was not declared in this scope 26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize); | ^~~~~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:26:51: error: expected primary-expression before ‘int’ 26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize); | ^~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:29:16: error: ‘mseq_t’ was not declared in this scope 29 | HHalignWrapper(mseq_t *mseq, int *piOrderLR, | ^~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:29:24: error: ‘mseq’ was not declared in this scope 29 | HHalignWrapper(mseq_t *mseq, int *piOrderLR, | ^~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:29:30: error: expected primary-expression before ‘int’ 29 | HHalignWrapper(mseq_t *mseq, int *piOrderLR, | ^~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:30:16: error: expected primary-expression before ‘double’ 30 | double *pdSeqWeights, int iNodeCount, | ^~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:30:38: error: expected primary-expression before ‘int’ 30 | double *pdSeqWeights, int iNodeCount, | ^~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:31:16: error: ‘hmm_light’ was not declared in this scope 31 | hmm_light *prHMMList, int iHMMCount, | ^~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:31:27: error: ‘prHMMList’ was not declared in this scope 31 | hmm_light *prHMMList, int iHMMCount, | ^~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:31:38: error: expected primary-expression before ‘int’ 31 | hmm_light *prHMMList, int iHMMCount, | ^~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:32:16: error: expected primary-expression before ‘int’ 32 | int iProfProfSeparator, hhalign_para rHhalignPara); | ^~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:32:40: error: ‘hhalign_para’ was not declared in this scope 32 | int iProfProfSeparator, hhalign_para rHhalignPara); | ^~~~~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:34:1: error: variable or field ‘SanitiseUnknown’ declared void 34 | SanitiseUnknown(mseq_t *mseq); | ^~~~~~~~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:34:17: error: ‘mseq_t’ was not declared in this scope 34 | SanitiseUnknown(mseq_t *mseq); | ^~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:34:25: error: ‘mseq’ was not declared in this scope 34 | SanitiseUnknown(mseq_t *mseq); | ^~~~ In file included from /usr/include/clustalo/clustal-omega.h:51, from /tmp/82Zk4_TBrb/dump1.h:25: /usr/include/clustalo/clustal/hhalign_wrapper.h:23:113: error: ‘int PosteriorProbabilities(mseq_t*, hmm_light, hhalign_para, char*)’ redeclared as different kind of entity 23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile); | ^ /usr/include/clustalo/clustal/hhalign_wrapper.h:23:1: note: previous declaration ‘int PosteriorProbabilities’ 23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile); | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:26:67: error: ‘double PileUp(mseq_t*, hhalign_para, int)’ redeclared as different kind of entity 26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize); | ^ /usr/include/clustalo/clustal/hhalign_wrapper.h:26:1: note: previous declaration ‘double PileUp’ 26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize); | ^~~~~~ /usr/include/clustalo/clustal/hhalign_wrapper.h:32:65: error: ‘double HHalignWrapper(mseq_t*, int*, double*, int, hmm_light*, int, int, hhalign_para)’ redeclared as different kind of entity 32 | int iProfProfSeparator, hhalign_para rHhalignPara); | ^ /usr/include/clustalo/clustal/hhalign_wrapper.h:29:1: note: previous declaration ‘double HHalignWrapper’ 29 | HHalignWrapper(mseq_t *mseq, int *piOrderLR, | ^~~~~~~~~~~~~~