Temporary header file '/tmp/GXH8rfUFpU/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/stdlib.h" #include "/usr/include/stdint.h" #include "/usr/include/arm-linux-gnueabihf/sys/types.h" #include "/usr/share/nimble/hts/hts/private/hts_concat.h" // add classes BGZF* tmp_add_class_0; _h* tmp_add_class_1; bgzf_cache_t* tmp_add_class_2; cram_fd* tmp_add_class_3; htsFormat* tmp_add_class_4; sam_hdr_t* tmp_add_class_5; sam_hrecs_t* tmp_add_class_6; The GCC parameters: gcc -fdump-lang-raw -fkeep-inline-functions -c -x c++ -fpermissive -w "/tmp/GXH8rfUFpU/dump1.h" In file included from /tmp/GXH8rfUFpU/dump1.h:15: /usr/share/nimble/hts/hts/private/hts_concat.h:210:9: error: ‘htsFile’ does not name a type 210 | typedef htsFile samFile; | ^~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:253:71: error: ‘int64’ has not been declared 253 | typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int64 *beg, int64 *end); | ^~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:253:83: error: ‘int64’ has not been declared 253 | typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int64 *beg, int64 *end); | ^~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:264:43: error: ‘hts_pos_t’ has not been declared 264 | int hts_idx_push(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t offset, int is_mapped); | ^~~~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:264:58: error: ‘hts_pos_t’ has not been declared 264 | int hts_idx_push(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t offset, int is_mapped); | ^~~~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:280:57: error: ‘hts_pos_t’ has not been declared 280 | hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec); | ^~~~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:280:72: error: ‘hts_pos_t’ has not been declared 280 | hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec); | ^~~~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:286:70: error: ‘hts_pos_t’ has not been declared 286 | typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec); | ^~~~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:286:85: error: ‘hts_pos_t’ has not been declared 286 | typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec); | ^~~~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:335:5: error: ‘hts_pos_t’ does not name a type; did you mean ‘hts_itr_t’? 335 | hts_pos_t pos; | ^~~~~~~~~ | hts_itr_t /usr/share/nimble/hts/hts/private/hts_concat.h:345:5: error: ‘hts_pos_t’ does not name a type; did you mean ‘hts_itr_t’? 345 | hts_pos_t mpos; | ^~~~~~~~~ | hts_itr_t /usr/share/nimble/hts/hts/private/hts_concat.h:346:5: error: ‘hts_pos_t’ does not name a type; did you mean ‘hts_itr_t’? 346 | hts_pos_t isize; | ^~~~~~~~~ | hts_itr_t /usr/share/nimble/hts/hts/private/hts_concat.h:362:25: error: ‘samFile’ was not declared in this scope 362 | sam_hdr_t *sam_hdr_read(samFile *fp); | ^~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:362:34: error: ‘fp’ was not declared in this scope 362 | sam_hdr_t *sam_hdr_read(samFile *fp); | ^~ /usr/share/nimble/hts/hts/private/hts_concat.h:370:15: error: ‘samFile’ was not declared in this scope 370 | int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b); | ^~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:370:24: error: ‘fp’ was not declared in this scope 370 | int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b); | ^~ /usr/share/nimble/hts/hts/private/hts_concat.h:370:38: error: expected primary-expression before ‘*’ token 370 | int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b); | ^ /usr/share/nimble/hts/hts/private/hts_concat.h:370:39: error: ‘h’ was not declared in this scope; did you mean ‘_h’? 370 | int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b); | ^ | _h /usr/share/nimble/hts/hts/private/hts_concat.h:370:49: error: expected primary-expression before ‘*’ token 370 | int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b); | ^ /usr/share/nimble/hts/hts/private/hts_concat.h:370:50: error: ‘b’ was not declared in this scope 370 | int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b); | ^ /usr/share/nimble/hts/hts/private/hts_concat.h:408:28: error: ‘samFile’ was not declared in this scope 408 | hts_idx_t * sam_index_load(samFile *in, char *); // load index | ^~~~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:408:37: error: ‘in’ was not declared in this scope; did you mean ‘int’? 408 | hts_idx_t * sam_index_load(samFile *in, char *); // load index | ^~ | int /usr/share/nimble/hts/hts/private/hts_concat.h:408:41: error: expected primary-expression before ‘char’ 408 | hts_idx_t * sam_index_load(samFile *in, char *); // load index | ^~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:579:5: error: ‘hts_pos_t’ does not name a type; did you mean ‘hts_itr_t’? 579 | hts_pos_t pos; // POS | ^~~~~~~~~ | hts_itr_t /usr/share/nimble/hts/hts/private/hts_concat.h:580:5: error: ‘hts_pos_t’ does not name a type; did you mean ‘hts_itr_t’? 580 | hts_pos_t rlen; // length of REF | ^~~~~~~~~ | hts_itr_t /usr/share/nimble/hts/hts/private/hts_concat.h:694:58: error: ‘int64’ has not been declared 694 | int bcf_readrec(BGZF *fp, void *null, void *v, int *tid, int64 *beg, int64 *end); | ^~~~~ /usr/share/nimble/hts/hts/private/hts_concat.h:694:70: error: ‘int64’ has not been declared 694 | int bcf_readrec(BGZF *fp, void *null, void *v, int *tid, int64 *beg, int64 *end); | ^~~~~