Closed shuaiwang2 closed 2 months ago
Hello, I want to report bug again when install grapes, could you help me again ? Looking forward to your response, very thanks.
cmake . make
-- The CXX compiler identification is GNU 11.4.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found /usr/bin/gzip compression program, using file extension .gz -- bpp-core3 1.0.0 found: -- static lib: not built/installed -- shared lib: /usr/local/lib/libbpp-core3.so.1.0.0 -- includes: /usr/local/include -- bpp-seq3 1.0.0 found: -- static lib: not built/installed -- shared lib: /usr/local/lib/libbpp-seq3.so.1.0.0 -- includes: /usr/local/include -- bpp-phyl3 1.0.0 found: -- static lib: not built/installed -- shared lib: /usr/local/lib/libbpp-phyl3.so.1.0.0 -- includes: /usr/local/include -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/include (found version "2.7.1") -- GSL libraries found here: -- includes: /usr/include -- dynamic libraries: /usr/lib/x86_64-linux-gnu/libgsl.so;/usr/lib/x86_64-linux-gnu/libgslcblas.so -- Configuring done -- Generating done -- Build files have been written to: /media/shuaiwang/3d/FileS1-master/grapes
/media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1872:50: error: expected class-name before ‘,’ token 1872 | class bpp_SFS_minus_lnl : public virtual Function, | ^ /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp: In function ‘double SFS_max_likelihood(bpp_SFS_minus_lnl, std::map<std::__cxx11::basic_string<char>, double>, bpp::ParameterList*, const string&)’: /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1959:55: error: no matching function for call to ‘bpp::ReparametrizationFunctionWrapper::ReparametrizationFunctionWrapper(bpp_SFS_minus_lnl*, bool)’ 1959 | ReparametrizationFunctionWrapper rpf(&lnL_fct, false); | ^ In file included from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:14: /usr/local/include/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h:61:3: note: candidate: ‘bpp::ReparametrizationFunctionWrapper::ReparametrizationFunctionWrapper(const bpp::ReparametrizationFunctionWrapper&)’ 61 | ReparametrizationFunctionWrapper(const ReparametrizationFunctionWrapper& rfw) : | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h:61:3: note: candidate expects 1 argument, 2 provided In file included from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:14: /usr/local/include/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h:53:3: note: candidate: ‘bpp::ReparametrizationFunctionWrapper::ReparametrizationFunctionWrapper(std::shared_ptr<bpp::FunctionInterface>, const bpp::ParameterList&, bool)’ 53 | ReparametrizationFunctionWrapper(std::shared_ptr<FunctionInterface> function, const ParameterList& parameters, bool verbose = true) : | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h:53:71: note: no known conversion for argument 1 from ‘bpp_SFS_minus_lnl*’ to ‘std::shared_ptr<bpp::FunctionInterface>’ 53 | ReparametrizationFunctionWrapper(std::shared_ptr<FunctionInterface> function, const ParameterList& parameters, bool verbose = true) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h:36:3: note: candidate: ‘bpp::ReparametrizationFunctionWrapper::ReparametrizationFunctionWrapper(std::shared_ptr<bpp::FunctionInterface>, bool)’ 36 | ReparametrizationFunctionWrapper(std::shared_ptr<FunctionInterface> function, bool verbose = true) : | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h:36:71: note: no known conversion for argument 1 from ‘bpp_SFS_minus_lnl*’ to ‘std::shared_ptr<bpp::FunctionInterface>’ 36 | ReparametrizationFunctionWrapper(std::shared_ptr<FunctionInterface> function, bool verbose = true) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1961:43: error: no matching function for call to ‘bpp::ThreePointsNumericalDerivative::ThreePointsNumericalDerivative(bpp::ReparametrizationFunctionWrapper*)’ 1961 | ThreePointsNumericalDerivative tpnd(&rpf); | ^ In file included from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:15: /usr/local/include/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h:75:3: note: candidate: ‘bpp::ThreePointsNumericalDerivative::ThreePointsNumericalDerivative(std::shared_ptr<bpp::SecondOrderDerivable>)’ 75 | ThreePointsNumericalDerivative(std::shared_ptr<SecondOrderDerivable> function) : | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h:75:72: note: no known conversion for argument 1 from ‘bpp::ReparametrizationFunctionWrapper*’ to ‘std::shared_ptr<bpp::SecondOrderDerivable>’ 75 | ThreePointsNumericalDerivative(std::shared_ptr<SecondOrderDerivable> function) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h:66:3: note: candidate: ‘bpp::ThreePointsNumericalDerivative::ThreePointsNumericalDerivative(std::shared_ptr<bpp::FirstOrderDerivable>)’ 66 | ThreePointsNumericalDerivative(std::shared_ptr<FirstOrderDerivable> function) : | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h:66:71: note: no known conversion for argument 1 from ‘bpp::ReparametrizationFunctionWrapper*’ to ‘std::shared_ptr<bpp::FirstOrderDerivable>’ 66 | ThreePointsNumericalDerivative(std::shared_ptr<FirstOrderDerivable> function) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h:57:3: note: candidate: ‘bpp::ThreePointsNumericalDerivative::ThreePointsNumericalDerivative(std::shared_ptr<bpp::FunctionInterface>)’ 57 | ThreePointsNumericalDerivative (std::shared_ptr<FunctionInterface> function) : | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h:57:70: note: no known conversion for argument 1 from ‘bpp::ReparametrizationFunctionWrapper*’ to ‘std::shared_ptr<bpp::FunctionInterface>’ 57 | ThreePointsNumericalDerivative (std::shared_ptr<FunctionInterface> function) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h:50:7: note: candidate: ‘bpp::ThreePointsNumericalDerivative::ThreePointsNumericalDerivative(const bpp::ThreePointsNumericalDerivative&)’ 50 | class ThreePointsNumericalDerivative : | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h:50:7: note: no known conversion for argument 1 from ‘bpp::ReparametrizationFunctionWrapper*’ to ‘const bpp::ThreePointsNumericalDerivative&’ /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1966:42: error: no matching function for call to ‘bpp::PseudoNewtonOptimizer::PseudoNewtonOptimizer(bpp::ThreePointsNumericalDerivative*)’ 1966 | optim = new PseudoNewtonOptimizer(&tpnd); | ^ In file included from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:19: /usr/local/include/Bpp/Phyl/PseudoNewtonOptimizer.h:58:3: note: candidate: ‘bpp::PseudoNewtonOptimizer::PseudoNewtonOptimizer(std::shared_ptr<bpp::SecondOrderDerivable>)’ 58 | PseudoNewtonOptimizer(std::shared_ptr<SecondOrderDerivable> function); | ^~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Phyl/PseudoNewtonOptimizer.h:58:63: note: no known conversion for argument 1 from ‘bpp::ThreePointsNumericalDerivative*’ to ‘std::shared_ptr<bpp::SecondOrderDerivable>’ 58 | PseudoNewtonOptimizer(std::shared_ptr<SecondOrderDerivable> function); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /usr/local/include/Bpp/Phyl/PseudoNewtonOptimizer.h:23:7: note: candidate: ‘bpp::PseudoNewtonOptimizer::PseudoNewtonOptimizer(const bpp::PseudoNewtonOptimizer&)’ 23 | class PseudoNewtonOptimizer : | ^~~~~~~~~~~~~~~~~~~~~ /usr/local/include/Bpp/Phyl/PseudoNewtonOptimizer.h:23:7: note: no known conversion for argument 1 from ‘bpp::ThreePointsNumericalDerivative*’ to ‘const bpp::PseudoNewtonOptimizer&’ /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1972:63: error: no matching function for call to ‘bpp::StlOutputStream::StlOutputStream(std::ofstream*)’ 1972 | new StlOutputStream(new ofstream(mhPath.c_str(), ios::out)); | ^ In file included from /usr/local/include/Bpp/App/ApplicationTools.h:10, from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:9: /usr/local/include/Bpp/Io/OutputStream.h:127:3: note: candidate: ‘bpp::StlOutputStream::StlOutputStream(const bpp::StlOutputStream&)’ 127 | StlOutputStream(const StlOutputStream& stlos) : stream_() { stream_ = std::move(stlos.stream_); } | ^~~~~~~~~~~~~~~ /usr/local/include/Bpp/Io/OutputStream.h:127:42: note: no known conversion for argument 1 from ‘std::ofstream*’ {aka ‘std::basic_ofstream<char>*’} to ‘const bpp::StlOutputStream&’ 127 | StlOutputStream(const StlOutputStream& stlos) : stream_() { stream_ = std::move(stlos.stream_); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /usr/local/include/Bpp/Io/OutputStream.h:126:3: note: candidate: ‘bpp::StlOutputStream::StlOutputStream(std::unique_ptr<std::basic_ostream<char> >)’ 126 | StlOutputStream(std::unique_ptr<std::ostream> stream) : stream_(std::move(stream)) {} | ^~~~~~~~~~~~~~~ /usr/local/include/Bpp/Io/OutputStream.h:126:49: note: no known conversion for argument 1 from ‘std::ofstream*’ {aka ‘std::basic_ofstream<char>*’} to ‘std::unique_ptr<std::basic_ostream<char> >’ 126 | StlOutputStream(std::unique_ptr<std::ostream> stream) : stream_(std::move(stream)) {} | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1979:63: error: no matching function for call to ‘bpp::StlOutputStream::StlOutputStream(std::ofstream*)’ 1979 | new StlOutputStream(new ofstream(prPath.c_str(), ios::out)); | ^ In file included from /usr/local/include/Bpp/App/ApplicationTools.h:10, from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:9: /usr/local/include/Bpp/Io/OutputStream.h:127:3: note: candidate: ‘bpp::StlOutputStream::StlOutputStream(const bpp::StlOutputStream&)’ 127 | StlOutputStream(const StlOutputStream& stlos) : stream_() { stream_ = std::move(stlos.stream_); } | ^~~~~~~~~~~~~~~ /usr/local/include/Bpp/Io/OutputStream.h:127:42: note: no known conversion for argument 1 from ‘std::ofstream*’ {aka ‘std::basic_ofstream<char>*’} to ‘const bpp::StlOutputStream&’ 127 | StlOutputStream(const StlOutputStream& stlos) : stream_() { stream_ = std::move(stlos.stream_); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /usr/local/include/Bpp/Io/OutputStream.h:126:3: note: candidate: ‘bpp::StlOutputStream::StlOutputStream(std::unique_ptr<std::basic_ostream<char> >)’ 126 | StlOutputStream(std::unique_ptr<std::ostream> stream) : stream_(std::move(stream)) {} | ^~~~~~~~~~~~~~~ /usr/local/include/Bpp/Io/OutputStream.h:126:49: note: no known conversion for argument 1 from ‘std::ofstream*’ {aka ‘std::basic_ofstream<char>*’} to ‘std::unique_ptr<std::basic_ostream<char> >’ 126 | StlOutputStream(std::unique_ptr<std::ostream> stream) : stream_(std::move(stream)) {} | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1985:22: error: cannot convert ‘bpp::OutputStream*’ to ‘std::shared_ptr<bpp::OutputStream>’ 1985 | optim->setProfiler(profiler); | ^~~~~~~~ | | | bpp::OutputStream* In file included from /usr/local/include/Bpp/Phyl/PseudoNewtonOptimizer.h:8, from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:19: /usr/local/include/Bpp/Numeric/Function/AbstractOptimizer.h:202:50: note: initializing argument 1 of ‘virtual void bpp::AbstractOptimizer::setProfiler(std::shared_ptr<bpp::OutputStream>)’ 202 | void setProfiler(std::shared_ptr<OutputStream> profiler) override { profiler_ = profiler; } | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1986:28: error: cannot convert ‘bpp::OutputStream*’ to ‘std::shared_ptr<bpp::OutputStream>’ 1986 | optim->setMessageHandler(messageHandler); | ^~~~~~~~~~~~~~ | | | bpp::OutputStream* In file included from /usr/local/include/Bpp/Phyl/PseudoNewtonOptimizer.h:8, from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:19: /usr/local/include/Bpp/Numeric/Function/AbstractOptimizer.h:198:56: note: initializing argument 1 of ‘virtual void bpp::AbstractOptimizer::setMessageHandler(std::shared_ptr<bpp::OutputStream>)’ 198 | void setMessageHandler(std::shared_ptr<OutputStream> mh) override { messageHandler_ = mh; } | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:1991:27: error: cannot convert ‘bpp::FunctionStopCondition’ to ‘std::shared_ptr<bpp::OptimizationStopCondition>’ 1991 | optim->setStopCondition(mystop); | ^~~~~~ | | | bpp::FunctionStopCondition In file included from /usr/local/include/Bpp/Phyl/PseudoNewtonOptimizer.h:8, from /media/shuaiwang/3d/FileS1-master/grapes/grapes/Grapes.cpp:19: /usr/local/include/Bpp/Numeric/Function/AbstractOptimizer.h:208:68: note: initializing argument 1 of ‘virtual void bpp::AbstractOptimizer::setStopCondition(std::shared_ptr<bpp::OptimizationStopCondition>)’ 208 | void setStopCondition(std::shared_ptr<OptimizationStopCondition> stopCondition) override | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ make[2]: *** [grapes/CMakeFiles/grapes.dir/build.make:76: grapes/CMakeFiles/grapes.dir/Grapes.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:127: grapes/CMakeFiles/grapes.dir/all] Error 2 make: *** [Makefile:156: all] Error 2
Hello, I want to report bug again when install grapes, could you help me again ? Looking forward to your response, very thanks.
cmake
make