Compiler warnings

[tseemann]

gcc --version
gcc (Homebrew gcc 5.3.0) 5.3.0

In file included from src/fqheader.h:21:0,
                 from src/fqfile.c:14:
/usr/include/zlib.h:1324:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s *'
 ZEXTERN int ZEXPORT gzwrite OF((gzFile file,
                     ^
src/fqfile.c: In function 'fqfile_eof_file_fastq_compressed':
src/fqfile.c:285:18: warning: passing argument 1 of 'gzeof' from incompatible pointer type [-Wincompatible-pointer-types]
     return gzeof((gzFile*)(((fqfile*)f)->handle));
                  ^
In file included from src/fqheader.h:21:0,
                 from src/fqfile.c:14:
/usr/include/zlib.h:1458:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s *'
 ZEXTERN int ZEXPORT gzeof OF((gzFile file));
                     ^
src/fqfile.c: In function 'fqfile_flush_file_fastq_compressed':
src/fqfile.c:302:13: warning: passing argument 1 of 'gzflush' from incompatible pointer type [-Wincompatible-pointer-types]
     gzflush((gzFile*)(((fqfile*)f)->handle), 0);
             ^
In file included from src/fqheader.h:21:0,
                 from src/fqfile.c:14:
/usr/include/zlib.h:1395:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s *'
 ZEXTERN int ZEXPORT gzflush OF((gzFile file, int flush));
                     ^
cc -O2 -g -Wall -Wextra -Wno-unused-parameter -I/bio/linuxbrew/opt/htslib/include  -c -o src/fqfsin.o src/fqfsin.c
cc -O2 -g -Wall -Wextra -Wno-unused-parameter -I/bio/linuxbrew/opt/htslib/include  -c -o src/fqfsout.o src/fqfsout.c
src/fqfsout.c: In function 'fqfsout_writechar':
src/fqfsout.c:165:14: warning: variable 'result' set but not used [-Wunused-but-set-variable]
     fqstatus result;
              ^
src/fqfsout.c: In function 'fqfsout_write':
src/fqfsout.c:178:14: warning: variable 'result' set but not used [-Wunused-but-set-variable]
     fqstatus result;
              ^
cc -O2 -g -Wall -Wextra -Wno-unused-parameter -I/bio/linuxbrew/opt/htslib/include  -c -o src/fqfileprep.o src/fqfileprep.c
src/fqfileprep.c: In function 'prepare_filesets':
src/fqfileprep.c:86:15: warning: 'informat_2' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if((outformat_2 == FQ_FORMAT_UNKNOWN) && (options.input_interleaving == FQ_INTERLEAVED)) outformat_2 = info
               ^

[yifangt]

I met this same issue when trying gzopen().
Have ever found a solution to get rid of the warnings? I appreciate if you could share your solution if you have. Thanks a lot!

[alastair-droop]

Hi. As I don't get any of these errors (even with all errors & warnings) on my Mac, this may take some time to work out.