[Debian-med-packaging] Bug#952102: salmon: FTBFS: SalmonAlevin.cpp:780:6: error: ‘class rapmap::utils::MappingConfig’ has no member named ‘maxSlack’

[Alberto Garcia]

On Sun, Feb 23, 2020 at 09:02:55AM +0100, Lucas Nussbaum wrote:

> > /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp: In function ‘void processReadsQuasi(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<rapmap::utils::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, RapMapIndexT*, std::vector<Transcript>&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, BiasParams&, SalmonOpts&, std::mutex&, bool, std::atomic<bool>&, volatile bool&, AlevinOpts<ProtocolT>&, SoftMapT&, spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>&)’:
> > /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp:780:6: error: ‘class rapmap::utils::MappingConfig’ has no member named ‘maxSlack’
> >   780 |   mc.maxSlack = salmonOpts.consensusSlack;
> >       |      ^~~~~~~~
> > make[4]: *** [src/CMakeFiles/salmon.dir/build.make:274: src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o] Error 1

This usage of mc.maxSlack was already removed upstream last year, see

   https://github.com/COMBINE-lab/salmon/commit/056f9c357a2b28ebcd5db923c53a1ea635bf88dd

I guess that the salmon package simply needs to be updated to the
most recent upstream version (latest is 1.1.0, Debian has 0.12.0 from
2018).

Berto