R CMD SHLIB -o fastGLOBETROTTERCompanion.so fastGLOBETROTTERCompanion.c -lz -O2 gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastGLOBETROTTERCompanion.c -o fastGLOBETROTTERCompanion.o fastGLOBETROTTERCompanion.c: In function ‘data_read’: fastGLOBETROTTERCompanion.c:230:7: warning: assignment to ‘FILE *’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 230 | fd2 = gzopen(filenameSAMP,"r"); | ^ fastGLOBETROTTERCompanion.c:232:28: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 232 | line_check=0; if (gzgets(fd2,line,2047)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:248:16: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types] 248 | while(!gzeof(fd2)) | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1598:34: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1598 | ZEXTERN int ZEXPORT gzeof(gzFile file); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:250:17: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 250 | if(gzgets(fd2,line,10000000)!=NULL); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:275:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 275 | gzclose(fd2); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:413:11: warning: assignment to ‘FILE *’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 413 | fd2 = gzopen(filenameSAMP,"r"); | ^ fastGLOBETROTTERCompanion.c:415:32: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 415 | line_check=0; if (gzgets(fd2,line,2047)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:423:40: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 423 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:436:40: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 436 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; // HAP label | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:440:44: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 440 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:463:44: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 463 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:572:15: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 572 | gzclose(fd2); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c: In function ‘data_read_null’: fastGLOBETROTTERCompanion.c:734:7: warning: assignment to ‘FILE *’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 734 | fd2 = gzopen(filenameSAMP,"r"); | ^ fastGLOBETROTTERCompanion.c:736:28: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 736 | line_check=0; if (gzgets(fd2,line,2047)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:752:16: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types] 752 | while(!gzeof(fd2)) | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1598:34: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1598 | ZEXTERN int ZEXPORT gzeof(gzFile file); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:754:17: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 754 | if(gzgets(fd2,line,10000000)!=NULL); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:779:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 779 | gzclose(fd2); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:868:11: warning: assignment to ‘FILE *’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 868 | fd2 = gzopen(filenameSAMP,"r"); | ^ fastGLOBETROTTERCompanion.c:870:32: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 870 | line_check=0; if (gzgets(fd2,line,2047)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:879:40: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 879 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:886:40: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 886 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; // HAP label | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:890:44: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 890 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:908:44: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 908 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:913:15: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 913 | gzclose(fd2); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c: In function ‘data_read_mode3’: fastGLOBETROTTERCompanion.c:1254:7: warning: assignment to ‘FILE *’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 1254 | fd2 = gzopen(filenameSAMP,"r"); | ^ fastGLOBETROTTERCompanion.c:1256:28: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 1256 | line_check=0; if (gzgets(fd2,line,2047)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1272:16: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types] 1272 | while(!gzeof(fd2)) | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1598:34: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1598 | ZEXTERN int ZEXPORT gzeof(gzFile file); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1274:17: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 1274 | if(gzgets(fd2,line,10000000)!=NULL); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1299:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 1299 | gzclose(fd2); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1413:11: warning: assignment to ‘FILE *’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 1413 | fd2 = gzopen(filenameSAMP,"r"); | ^ fastGLOBETROTTERCompanion.c:1415:32: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 1415 | line_check=0; if (gzgets(fd2,line,2047)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1423:40: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 1423 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1436:40: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 1436 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; // HAP label | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1440:44: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 1440 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1459:44: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 1459 | line_check=0; if (gzgets(fd2,line,10000000)!=NULL) line_check=1; | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len); | ~~~~~~~^~~~ fastGLOBETROTTERCompanion.c:1547:15: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 1547 | gzclose(fd2); | ^~~ | | | FILE * In file included from fastGLOBETROTTERCompanion.c:7: /usr/local/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘FILE *’ 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o fastGLOBETROTTERCompanion.so fastGLOBETROTTERCompanion.o -lz -O2 -L/usr/lib/R/lib -lR