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
