[Debian-med-packaging] Bug#813465: Bug#813465: bcftools: FTBFS: vcfmerge.c:424:6: error: conflicting types for 'bcf_hdr_merge'

[Sascha Steinbiss]

This is most likely related to the htslib 1.3 upgrade. I expect that
updating bcftools to the most recent upstream release (1.3) as well will
help.

On 02/02/2016 09:49, Chris Lamb wrote:
> Source: bcftools
> Version: 1.2-2
> Severity: serious
> Justification: fails to build from source
> User: reproducible-builds at lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org
> 
> Dear Maintainer,
> 
> bcftools fails to build from source in unstable/amd64:
> 
>   [..]
> 
>   cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/x86_64-linux-gnu/bcftools\" -DUSE_GPL  -I. -I/usr/include vcfsom.c -o vcfsom.o
>   vcfmerge.c:424:6: error: conflicting types for 'bcf_hdr_merge'
>    void bcf_hdr_merge(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples)
>         ^
>   In file included from vcfmerge.c:30:0:
>   /usr/include/htslib/vcf.h:407:16: note: previous declaration of 'bcf_hdr_merge' was here
>        bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src);
>                   ^
>   vcfmerge.c: In function 'bcf_hdr_merge':
>   vcfmerge.c:427:5: warning: 'bcf_hdr_combine' is deprecated: Please use bcf_hdr_merge instead [-Wdeprecated-declarations]
>        int ret = bcf_hdr_combine(hw, hr);
>        ^
>   In file included from vcfmerge.c:30:0:
>   /usr/include/htslib/vcf.h:391:9: note: declared here
>        int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src) HTS_DEPRECATED("Please use bcf_hdr_merge instead");
>            ^
>   Makefile:90: recipe for target 'vcfmerge.o' failed
>   make[1]: *** [vcfmerge.o] Error 1
>   make[1]: *** Waiting for unfinished jobs....
>   make[1]: Leaving directory '/home/lamby/temp/cdt.20160202103852.cx8O6CogYx/bcftools-1.2'
>   dh_auto_build: make -j9 returned exit code 2
>   debian/rules:15: recipe for target 'build' failed
>   make: *** [build] Error 2
> 
>   [..]
> 
> The full build log is attached.
> 
> 
> Regards,
> 
> 
> 
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> 


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