Source: bppsuite Version: 0.8.0-1+build1 Severity: serious Justification: fails to build from source
Hi, bppsuite FTBFS with GCC 5 building against the C++v5 transitioned bpp libraries: https://buildd.debian.org/status/fetch.php?pkg=bppsuite&arch=amd64&ver=0.8.0-1%2Bbuild1%2Bb1&stamp=1464293213 make[3]: Entering directory '/«PKGBUILDDIR»' [ 37%] Building CXX object bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp: In function 'int main(int, char**)': /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:204:118: error: no matching function for call to 'bpp::PhylogeneticsApplicationTools::getSubstitutionModel(bpp::Alphabet*&, int, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)' SubstitutionModel* model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, 0, bppseqgen.getParams()); ^ In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0: /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: candidate: static bpp::SubstitutionModel* bpp::PhylogeneticsApplicationTools::getSubstitutionModel(const bpp::Alphabet*, const bpp::GeneticCode*, const bpp::SiteContainer*, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const string&, bool, bool, int) static SubstitutionModel* getSubstitutionModel( ^ /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: candidate expects 8 arguments, 3 provided /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:205:97: error: no matching function for call to 'bpp::FixedFrequenciesSet::FixedFrequenciesSet(const bpp::Alphabet*, const Vdouble&)' FrequenciesSet* fSet = new FixedFrequenciesSet(model->getAlphabet(), model->getFrequencies()); ^ In file included from /usr/include/Bpp/Phyl/Model/SubstitutionModel.h:43:0, from /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:45, from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63: /usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:332:3: note: candidate: bpp::FixedFrequenciesSet::FixedFrequenciesSet(bpp::StateMap*, const string&) FixedFrequenciesSet(StateMap* stateMap, const std::string& name = "Fixed"); ^ /usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:332:3: note: no known conversion for argument 1 from 'const bpp::Alphabet*' to 'bpp::StateMap*' /usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:324:3: note: candidate: bpp::FixedFrequenciesSet::FixedFrequenciesSet(bpp::StateMap*, const std::vector<double, std::allocator<double> >&, const string&) FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception); ^ /usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:324:3: note: no known conversion for argument 1 from 'const bpp::Alphabet*' to 'bpp::StateMap*' /usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:311:7: note: candidate: bpp::FixedFrequenciesSet::FixedFrequenciesSet(const bpp::FixedFrequenciesSet&) class FixedFrequenciesSet : ^ /usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:311:7: note: candidate expects 1 argument, 2 provided /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:216:101: error: no matching function for call to 'bpp::PhylogeneticsApplicationTools::getSubstitutionModel(bpp::Alphabet*&, int, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)' model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, 0, bppseqgen.getParams()); ^ In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0: /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: candidate: static bpp::SubstitutionModel* bpp::PhylogeneticsApplicationTools::getSubstitutionModel(const bpp::Alphabet*, const bpp::GeneticCode*, const bpp::SiteContainer*, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const string&, bool, bool, int) static SubstitutionModel* getSubstitutionModel( ^ /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: candidate expects 8 arguments, 3 provided /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:222:111: error: no matching function for call to 'bpp::PhylogeneticsApplicationTools::getSubstitutionModel(bpp::Alphabet*&, bpp::VectorSiteContainer*&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)' model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, allSitesAln, bppseqgen.getParams()); ^ In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0: /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: candidate: static bpp::SubstitutionModel* bpp::PhylogeneticsApplicationTools::getSubstitutionModel(const bpp::Alphabet*, const bpp::GeneticCode*, const bpp::SiteContainer*, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const string&, bool, bool, int) static SubstitutionModel* getSubstitutionModel( ^ /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: candidate expects 8 arguments, 3 provided /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:234:131: error: no matching function for call to 'bpp::PhylogeneticsApplicationTools::getRootFrequenciesSet(bpp::Alphabet*&, int, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, std::vector<double, std::allocator<double> >&)' FrequenciesSet* rootFreqs = PhylogeneticsApplicationTools::getRootFrequenciesSet(alphabet, 0, bppseqgen.getParams(), rateFreqs); ^ In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0: /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:218:28: note: candidate: static bpp::FrequenciesSet* bpp::PhylogeneticsApplicationTools::getRootFrequenciesSet(const bpp::Alphabet*, const bpp::GeneticCode*, const bpp::SiteContainer*, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const std::vector<double, std::allocator<double> >&, const string&, bool, bool, int) static FrequenciesSet* getRootFrequenciesSet( ^ /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:218:28: note: candidate expects 9 arguments, 4 provided /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:250:106: error: no matching function for call to 'bpp::PhylogeneticsApplicationTools::getSubstitutionModelSet(bpp::Alphabet*&, int, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)' modelSet = PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, 0, bppseqgen.getParams()); ^ In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0: /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:263:35: note: candidate: static bpp::SubstitutionModelSet* bpp::PhylogeneticsApplicationTools::getSubstitutionModelSet(const bpp::Alphabet*, const bpp::GeneticCode*, const bpp::SiteContainer*, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const string&, bool, bool, int) static SubstitutionModelSet* getSubstitutionModelSet( ^ /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:263:35: note: candidate expects 8 arguments, 3 provided /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:256:117: error: no matching function for call to 'bpp::PhylogeneticsApplicationTools::getSubstitutionModelSet(bpp::Alphabet*&, bpp::VectorSiteContainer*&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)' modelSet = PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, allSitesAln, bppseqgen.getParams()); ^ In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0: /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:263:35: note: candidate: static bpp::SubstitutionModelSet* bpp::PhylogeneticsApplicationTools::getSubstitutionModelSet(const bpp::Alphabet*, const bpp::GeneticCode*, const bpp::SiteContainer*, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const string&, bool, bool, int) static SubstitutionModelSet* getSubstitutionModelSet( ^ /usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:263:35: note: candidate expects 8 arguments, 3 provided bppSuite/CMakeFiles/bppseqgen.dir/build.make:62: recipe for target 'bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o' failed make[3]: *** [bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o] Error 1 make[3]: Leaving directory '/«PKGBUILDDIR»' Andreas
