[Debian-med-packaging] Bug#818397: salmon: FTBFS: 'MEM_F_SELF_OVLP' was not declared in this scope

[Sascha Steinbiss]

Hi,

I have pushed a fix for this to git. I would be glad if someone could take a look.

Thanks
Sascha

On Wed, 16 Mar 2016 13:36:46 -0700 Martin Michlmayr <tbm at hpe.com> wrote:
> Package: salmon
> Version: 0.4.2+ds1-2
> Severity: serious
> 
> This package fails to build in unstable:
> 
> > sbuild (Debian sbuild) 0.68.0 (15 Jan 2016) on dl580gen9-02.hlinux
> ...
> > /<<BUILDDIR>>/salmon-0.4.2+ds1/src/CollapsedGibbsSampler.cpp: In function 'void sampleRound_(std::vector<std::pair<const TranscriptGroup, TGValue> >&, std::vector<int>&, std::vector<double>&, double, std::vector<int>&, MultinomialSampler&)':
> > /<<BUILDDIR>>/salmon-0.4.2+ds1/src/CollapsedGibbsSampler.cpp:119:18: warning: unused variable 'classCount' [-Wunused-variable]
> >          uint64_t classCount = eqClass.second.count;
> >                   ^
> > /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonQuantify.cpp: In function 'void mem_collect_intv(const SalmonOpts&, const mem_opt_t*, const bwt_t*, int, const uint8_t*, smem_aux_t*)':
> > /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonQuantify.cpp:159:36: error: 'MEM_F_SELF_OVLP' was not declared in this scope
> >      int start_width = (opt->flag & MEM_F_SELF_OVLP)? 2 : 1;
> 
> -- 
> Martin Michlmayr
> Linux for HPE Helion, Hewlett Packard Enterprise
> 
>