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

[Dominique Belhachemi]

On Sun, 27 Apr 2014 16:48:52 +0100 Michael Tautschnig <mt at debian.org> wrote:
> 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
>

Hi Michael,

Does this still happen with htslib 1.1 ?
How can we reproduce this? Which compiler did you use? Which architecture?

Best
-Dominique
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