On Sun, 27 Apr 2014 16:48:52 +0100 Michael Tautschnig <m...@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
