[Debian-med-packaging] Bug#746164: Conflicting declarations of function ks_init

[Michael Tautschnig]

Package: htslib
Version: 0.2.0~rc3-1
Usertags: goto-cc

While compiling the package using our research compiler infrastructure the build
failed with the following error:

[...]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -pthread -Wl,-z,relro -o test/fieldarith test/fieldarith.o libhts.a  -lz
file vcf.c line 19: error: conflicting function declarations "ks_init"
old definition in module hts file hts.c line 18
struct __kstream_t * (struct BGZF *f)
new definition in module vcf file vcf.c line 19
struct __kstream_t * (struct gzFile_s *)
make[2]: *** [test/fieldarith] Error 64

Looking at the source, the define of KS_BGZF may the cause:

http://sources.debian.net/src/htslib/0.2.0~rc3-1/hts.c?hl=15,16,17,18,19,20,21#L15

Note that the build does FTFBS with the standard compiler, as no type checking
at link time would be performed. Yet the use of ks_init may be severely broken.

Best,
Michael

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