* installing *source* package ‘galamm’ ... ** package ‘galamm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/galamm/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c compute_galamm.cpp -o compute_galamm.o compute_galamm.cpp: In instantiation of 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >]': compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:446:28: required from here compute_galamm.cpp:97:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > >, std::default_delete<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > > > >, std::allocator<std::unique_ptr<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > >, std::default_delete<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > > > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 97 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ compute_galamm.cpp:116:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > >, std::default_delete<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > > > >, std::allocator<std::unique_ptr<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > >, std::default_delete<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > > > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 116 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ compute_galamm.cpp:130:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > >, std::default_delete<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > > > >, std::allocator<std::unique_ptr<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > >, std::default_delete<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > > > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 130 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ compute_galamm.cpp: In instantiation of 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = autodiff::detail::Dual<double, double>]': compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = autodiff::detail::Dual<double, double>; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:452:28: required from here compute_galamm.cpp:97:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<autodiff::detail::Dual<double, double> >, std::default_delete<Model<autodiff::detail::Dual<double, double> > > >, std::allocator<std::unique_ptr<Model<autodiff::detail::Dual<double, double> >, std::default_delete<Model<autodiff::detail::Dual<double, double> > > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 97 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ compute_galamm.cpp:116:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<autodiff::detail::Dual<double, double> >, std::default_delete<Model<autodiff::detail::Dual<double, double> > > >, std::allocator<std::unique_ptr<Model<autodiff::detail::Dual<double, double> >, std::default_delete<Model<autodiff::detail::Dual<double, double> > > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 116 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ compute_galamm.cpp:130:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<autodiff::detail::Dual<double, double> >, std::default_delete<Model<autodiff::detail::Dual<double, double> > > >, std::allocator<std::unique_ptr<Model<autodiff::detail::Dual<double, double> >, std::default_delete<Model<autodiff::detail::Dual<double, double> > > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 130 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ compute_galamm.cpp: In instantiation of 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = double]': compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = double; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:458:27: required from here compute_galamm.cpp:97:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<double>, std::default_delete<Model<double> > >, std::allocator<std::unique_ptr<Model<double>, std::default_delete<Model<double> > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 97 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ compute_galamm.cpp:116:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<double>, std::default_delete<Model<double> > >, std::allocator<std::unique_ptr<Model<double>, std::default_delete<Model<double> > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 116 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ compute_galamm.cpp:130:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<double>, std::default_delete<Model<double> > >, std::allocator<std::unique_ptr<Model<double>, std::default_delete<Model<double> > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 130 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ In file included from compute_galamm.cpp:6: update_funs.h: In instantiation of 'void update_Zt(SpMdual<T>&, Vdual<T>&, const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >; SpMdual<T> = Eigen::SparseMatrix<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >, 0, int>; Vdual<T> = Eigen::Matrix<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >, -1, 1, 0, -1, 1>]': compute_galamm.cpp:88:12: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:446:28: required from here update_funs.h:117:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare] 117 | for(size_t k{}; k < Zt.outerSize(); ++k){ | ~~^~~~~~~~~~~~~~~~ update_funs.h: In instantiation of 'void update_X(Mdual<T>&, Vdual<T>&, const Eigen::VectorXi&) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >; Mdual<T> = Eigen::Matrix<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >, -1, -1, 0, -1, -1>; Vdual<T> = Eigen::Matrix<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >, -1, 1, 0, -1, 1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]': compute_galamm.cpp:89:11: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:446:28: required from here update_funs.h:64:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase<Eigen::Matrix<int, -1, 1> >::Index' {aka 'long int'} [-Wsign-compare] 64 | for(size_t i{}; i < lambda_mapping_X.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ compute_galamm.cpp: In instantiation of 'T loss(const parameters<T>&, const data<T>&, Vdual<T>&, std::vector<std::unique_ptr<Model<T> > >&, ldlt<T>&, Vdual<T>&) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >; Vdual<T> = Eigen::Matrix<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >, -1, 1, 0, -1, 1>; ldlt<T> = Eigen::SimplicialLDLT<Eigen::SparseMatrix<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >, 0, int>, 1, Eigen::AMDOrdering<int> >]': compute_galamm.cpp:110:31: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> >; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:446:28: required from here compute_galamm.cpp:36:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > >, std::default_delete<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > > > >, std::allocator<std::unique_ptr<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > >, std::default_delete<Model<autodiff::detail::Dual<autodiff::detail::Dual<double, double>, autodiff::detail::Dual<double, double> > > > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 36 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ update_funs.h: In instantiation of 'void update_Zt(SpMdual<T>&, Vdual<T>&, const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&) [with T = autodiff::detail::Dual<double, double>; SpMdual<T> = Eigen::SparseMatrix<autodiff::detail::Dual<double, double>, 0, int>; Vdual<T> = Eigen::Matrix<autodiff::detail::Dual<double, double>, -1, 1, 0, -1, 1>]': compute_galamm.cpp:88:12: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = autodiff::detail::Dual<double, double>]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = autodiff::detail::Dual<double, double>; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:452:28: required from here update_funs.h:117:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare] 117 | for(size_t k{}; k < Zt.outerSize(); ++k){ | ~~^~~~~~~~~~~~~~~~ update_funs.h: In instantiation of 'void update_X(Mdual<T>&, Vdual<T>&, const Eigen::VectorXi&) [with T = autodiff::detail::Dual<double, double>; Mdual<T> = Eigen::Matrix<autodiff::detail::Dual<double, double>, -1, -1, 0, -1, -1>; Vdual<T> = Eigen::Matrix<autodiff::detail::Dual<double, double>, -1, 1, 0, -1, 1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]': compute_galamm.cpp:89:11: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = autodiff::detail::Dual<double, double>]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = autodiff::detail::Dual<double, double>; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:452:28: required from here update_funs.h:64:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase<Eigen::Matrix<int, -1, 1> >::Index' {aka 'long int'} [-Wsign-compare] 64 | for(size_t i{}; i < lambda_mapping_X.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ compute_galamm.cpp: In instantiation of 'T loss(const parameters<T>&, const data<T>&, Vdual<T>&, std::vector<std::unique_ptr<Model<T> > >&, ldlt<T>&, Vdual<T>&) [with T = autodiff::detail::Dual<double, double>; Vdual<T> = Eigen::Matrix<autodiff::detail::Dual<double, double>, -1, 1, 0, -1, 1>; ldlt<T> = Eigen::SimplicialLDLT<Eigen::SparseMatrix<autodiff::detail::Dual<double, double>, 0, int>, 1, Eigen::AMDOrdering<int> >]': compute_galamm.cpp:110:31: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = autodiff::detail::Dual<double, double>]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = autodiff::detail::Dual<double, double>; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:452:28: required from here compute_galamm.cpp:36:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<autodiff::detail::Dual<double, double> >, std::default_delete<Model<autodiff::detail::Dual<double, double> > > >, std::allocator<std::unique_ptr<Model<autodiff::detail::Dual<double, double> >, std::default_delete<Model<autodiff::detail::Dual<double, double> > > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 36 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ update_funs.h: In instantiation of 'void update_Zt(SpMdual<T>&, Vdual<T>&, const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&) [with T = double; SpMdual<T> = Eigen::SparseMatrix<double, 0, int>; Vdual<T> = Eigen::Matrix<double, -1, 1>]': compute_galamm.cpp:88:12: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = double]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = double; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:458:27: required from here update_funs.h:117:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare] 117 | for(size_t k{}; k < Zt.outerSize(); ++k){ | ~~^~~~~~~~~~~~~~~~ update_funs.h: In instantiation of 'void update_X(Mdual<T>&, Vdual<T>&, const Eigen::VectorXi&) [with T = double; Mdual<T> = Eigen::Matrix<double, -1, -1>; Vdual<T> = Eigen::Matrix<double, -1, 1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]': compute_galamm.cpp:89:11: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = double]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = double; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:458:27: required from here update_funs.h:64:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase<Eigen::Matrix<int, -1, 1> >::Index' {aka 'long int'} [-Wsign-compare] 64 | for(size_t i{}; i < lambda_mapping_X.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ compute_galamm.cpp: In instantiation of 'T loss(const parameters<T>&, const data<T>&, Vdual<T>&, std::vector<std::unique_ptr<Model<T> > >&, ldlt<T>&, Vdual<T>&) [with T = double; Vdual<T> = Eigen::Matrix<double, -1, 1>; ldlt<T> = Eigen::SimplicialLDLT<Eigen::SparseMatrix<double, 0, int>, 1, Eigen::AMDOrdering<int> >]': compute_galamm.cpp:110:31: required from 'logLikObject<T> logLik(parameters<T>, data<T>, std::vector<std::unique_ptr<Model<T> > >&) [with T = double]' compute_galamm.cpp:305:22: required from 'Rcpp::List wrapper(const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::SparseMatrix<double, 0, int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const std::vector<int>&, const Eigen::VectorXd&, const Eigen::VectorXd&, const Eigen::VectorXi&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> >&, const Eigen::VectorXd&, const std::vector<int>&, const std::vector<std::__cxx11::basic_string<char> >&, const Eigen::VectorXi&, const Eigen::VectorXd&, const int&, const double&, bool) [with T = double; Rcpp::List = Rcpp::Vector<19>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>; Eigen::VectorXi = Eigen::Matrix<int, -1, 1>]' compute_galamm.cpp:458:27: required from here compute_galamm.cpp:36:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::unique_ptr<Model<double>, std::default_delete<Model<double> > >, std::allocator<std::unique_ptr<Model<double>, std::default_delete<Model<double> > > > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 36 | for(int k{}; k < modvec.size(); k++){ | ~~^~~~~~~~~~~~~~~ g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o galamm.so RcppExports.o compute_galamm.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/galamm/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/galamm/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/galamm/src' installing to /data/gannet/ripley/R/packages/tests-devel/galamm.Rcheck/00LOCK-galamm/00new/galamm/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (galamm)