* installing *source* package ‘glmmrOptim’ ...
** this is package ‘glmmrOptim’ version ‘0.3.6’
** package ‘glmmrOptim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/glmmrOptim/src'
g++ -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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/glmmrBase/include' -I'/data/gannet/ripley/R/test-dev/SparseChol/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/rminqa/include' -I/usr/local/include -fopenmp -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
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:4,
from ../inst/include/optim/optimdata.h:4,
from ../inst/include/optim/optimclass.h:7,
from ../inst/include/glmmrOptim.h:6,
from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:21:9: warning: ‘EIGEN_DEFAULT_DENSE_INDEX_TYPE’ redefined
21 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:19,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Dense:1,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigenForward.h:28,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
from ../inst/include/glmmrOptim.h:4:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: this is the location of the previous definition
33 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/glmmrBase/include' -I'/data/gannet/ripley/R/test-dev/SparseChol/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/rminqa/include' -I/usr/local/include -fopenmp -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 gd_search.cpp -o gd_search.o
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h:6,
from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:5,
from gd_search.cpp:1:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:21:9: warning: ‘EIGEN_DEFAULT_DENSE_INDEX_TYPE’ redefined
21 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:19,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Dense:1,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigenForward.h:28,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:10:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: this is the location of the previous definition
33 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/interpreter.h:4,
from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:6,
from ../inst/include/optim/optimderivatives.h:4,
from ../inst/include/optim/optimclass.h:8:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp: In member function ‘void glmmr::calculator::update_parameters(const dblvec&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1186:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1186 | for(int i = 0; i < parameter_indexes.size(); i++)parameters[i] = parameters_in[parameter_indexes[i]];
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp: In member function ‘void glmmr::calculator::print_instructions() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1457:30: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘const int’} and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1457 | if(indexes[idx_iter] >= parameter_names.size()){
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1472:30: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘const int’} and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1472 | if(indexes[idx_iter] >= data_names.size()){
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:6,
from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:7:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h: In function ‘bool glmmr::is_number(const std::string&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:12:11: warning: unused variable ‘a’ [-Wunused-variable]
12 | float a = std::stod(s);
| ^
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h: In function ‘void glmmr::two_way_fn(std::vector<char>&, calculator&, const Eigen::ArrayXXd&, const strvec&, Eigen::MatrixXd&, int, bool)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:235:19: warning: variable ‘variable_in_data’ set but not used [-Wunused-but-set-variable]
235 | bool add_check, variable_in_data;
| ^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘virtual int glmmr::Covariance::parse()’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:362:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
362 | for(k = 0; k < fnvars[idx].size(); k++){
| ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:376:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
376 | for(j = 0; j< fnvars.size();j++){
| ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:377:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
377 | for(k = 0; k < fnvars[j].size();k++){
| ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:395:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
395 | for(int m = 0; m < fnvars.size(); m++){
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:397:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
397 | for(int p = 0; p < fnvars[m].size(); p++){
| ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:404:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
404 | for(j = 0; j < groups.size(); j++){
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:417:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
417 | for(int m = 0; m < vals.size(); m++) vals[m] = data_(k,fnvars[idx][m]);
| ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:443:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
443 | for(int j = 0; j < fn_.size(); j++){
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:449:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
449 | for(int k = 0; k < fn_[j].size(); k++) fn_name += covfunc_to_str.at(fn_[j][k]);
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:450:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
450 | for(int k = 0; k < fn_[j].size(); k++){
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:474:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
474 | for(int i =0; i<fn_.size();i++){
| ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:475:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
475 | for(int j = 0; j < re_pars_[i].size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:476:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
476 | for(int k = 0; k < re_pars_[i][j].size(); k++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:484:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
484 | for(int i =0; i<fn_.size();i++){
| ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:491:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
491 | for(int j = 0; j<fn_[i].size();j++){
| ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:495:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
495 | for(int j = 0; j<fn_[i].size();j++){
| ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:518:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
518 | for(int k = 0; k < re_pars_[i][j].size(); k++)re_par_less_min_[k] -= minvalue;
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:524:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
524 | for(int j = 0; j < (fn_[i].size()-1); j++){
| ~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:539:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::calculator>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
539 | for(int i = 0; i < calc_.size(); i++){
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:546:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::calculator>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
546 | for(int i = 0; i < calc_.size(); i++) re_count_[re_order_[i]] += re_temp_data_[i].size();
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘void glmmr::Covariance::Z_updater()’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:614:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::ZNonZero>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
614 | for(int i = 0; i < z_nonzero.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:615:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
615 | for(int j = 0; j < z_nonzero[i].rows.size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘virtual void glmmr::Covariance::update_parameters(const Eigen::ArrayXd&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:718:32: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Array<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
718 | } else if(parameters_.size() == parameters.size()){
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::any_group_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1024:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1024 | for(int i = 0; i < fn_.size(); i++){
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::all_group_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1037:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1037 | for (int i = 0; i < fn_.size(); i++) {
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1038:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1038 | for (int j = 0; j < fn_[i].size(); j++) {
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::all_log_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1048:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1048 | for (int i = 0; i < fn_.size(); i++) {
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1049:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1049 | for (int j = 0; j < fn_[i].size(); j++) {
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::any_log_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1061:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1061 | for(int i = 0; i < fn_.size(); i++){
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘strvec glmmr::Covariance::parameter_names()’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1212:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1212 | for(int i = 0; i < form_.re_.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~
../inst/include/optim/optimderivatives.h: In member function ‘void glmmr::OptimDerivatives::addDesign(glmmr::Covariance&, bool)’:
../inst/include/optim/optimderivatives.h:22:9: warning: unused variable ‘curr_size’ [-Wunused-variable]
22 | int curr_size = FirstOrderDerivatives.size();
| ^~~~~~~~~
../inst/include/optim/optimclass.h: In member function ‘Eigen::MatrixXd glmmr::OptimDesign::KR_correction(const Eigen::MatrixXd&, const int&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::ArrayXi&)’:
../inst/include/optim/optimclass.h:129:9: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<glmmr::MatrixField<Eigen::Matrix<double, -1, -1> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
129 | if(idx>=derivs_.FirstOrderDerivatives.size() )Rcpp::stop("idx out of range");
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h: In instantiation of ‘T glmmr::MatrixField<T>::operator()(int) const [with T = Eigen::Matrix<double, -1, -1>]’:
../inst/include/optim/optimclass.h:148:54: required from here
148 | partial1 = Z*derivs_.FirstOrderDerivatives[idx](i)*Z.transpose();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:38:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unique_ptr<Eigen::Matrix<double, -1, -1>, std::default_delete<Eigen::Matrix<double, -1, -1> > >, std::allocator<std::unique_ptr<Eigen::Matrix<double, -1, -1>, std::default_delete<Eigen::Matrix<double, -1, -1> > > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
38 | if(i >= data.size()) throw std::runtime_error("Accessing index out of range matrix field");
| ~~^~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/interpreter.h:4,
from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp: In member function ‘void glmmr::calculator::update_parameters(const dblvec&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1186:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1186 | for(int i = 0; i < parameter_indexes.size(); i++)parameters[i] = parameters_in[parameter_indexes[i]];
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h: In instantiation of ‘T glmmr::MatrixField<T>::operator()(int) const [with T = Eigen::Matrix<double, -1, 1>]’:
../inst/include/optim/optimclass.h:269:42: required from here
269 | vals(j) = c_obj_fun( M, data_.C_list_(j));
| ~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:38:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unique_ptr<Eigen::Matrix<double, -1, 1>, std::default_delete<Eigen::Matrix<double, -1, 1> > >, std::allocator<std::unique_ptr<Eigen::Matrix<double, -1, 1>, std::default_delete<Eigen::Matrix<double, -1, 1> > > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
38 | if(i >= data.size()) throw std::runtime_error("Accessing index out of range matrix field");
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp: In member function ‘void glmmr::calculator::print_instructions() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1457:30: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘const int’} and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1457 | if(indexes[idx_iter] >= parameter_names.size()){
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1472:30: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘const int’} and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1472 | if(indexes[idx_iter] >= data_names.size()){
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:6,
from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:7:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h: In function ‘bool glmmr::is_number(const std::string&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:12:11: warning: unused variable ‘a’ [-Wunused-variable]
12 | float a = std::stod(s);
| ^
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h: In function ‘void glmmr::two_way_fn(std::vector<char>&, calculator&, const Eigen::ArrayXXd&, const strvec&, Eigen::MatrixXd&, int, bool)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:235:19: warning: variable ‘variable_in_data’ set but not used [-Wunused-but-set-variable]
235 | bool add_check, variable_in_data;
| ^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘virtual int glmmr::Covariance::parse()’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:362:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
362 | for(k = 0; k < fnvars[idx].size(); k++){
| ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:376:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
376 | for(j = 0; j< fnvars.size();j++){
| ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:377:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
377 | for(k = 0; k < fnvars[j].size();k++){
| ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:395:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
395 | for(int m = 0; m < fnvars.size(); m++){
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:397:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
397 | for(int p = 0; p < fnvars[m].size(); p++){
| ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:404:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
404 | for(j = 0; j < groups.size(); j++){
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:417:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
417 | for(int m = 0; m < vals.size(); m++) vals[m] = data_(k,fnvars[idx][m]);
| ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:443:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
443 | for(int j = 0; j < fn_.size(); j++){
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:449:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
449 | for(int k = 0; k < fn_[j].size(); k++) fn_name += covfunc_to_str.at(fn_[j][k]);
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:450:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
450 | for(int k = 0; k < fn_[j].size(); k++){
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:474:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
474 | for(int i =0; i<fn_.size();i++){
| ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:475:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
475 | for(int j = 0; j < re_pars_[i].size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:476:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
476 | for(int k = 0; k < re_pars_[i][j].size(); k++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:484:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
484 | for(int i =0; i<fn_.size();i++){
| ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:491:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
491 | for(int j = 0; j<fn_[i].size();j++){
| ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:495:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
495 | for(int j = 0; j<fn_[i].size();j++){
| ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:518:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
518 | for(int k = 0; k < re_pars_[i][j].size(); k++)re_par_less_min_[k] -= minvalue;
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:524:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
524 | for(int j = 0; j < (fn_[i].size()-1); j++){
| ~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:539:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::calculator>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
539 | for(int i = 0; i < calc_.size(); i++){
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:546:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::calculator>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
546 | for(int i = 0; i < calc_.size(); i++) re_count_[re_order_[i]] += re_temp_data_[i].size();
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘void glmmr::Covariance::Z_updater()’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:614:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::ZNonZero>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
614 | for(int i = 0; i < z_nonzero.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:615:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
615 | for(int j = 0; j < z_nonzero[i].rows.size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘virtual void glmmr::Covariance::update_parameters(const Eigen::ArrayXd&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:718:32: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Array<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
718 | } else if(parameters_.size() == parameters.size()){
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::any_group_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1024:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1024 | for(int i = 0; i < fn_.size(); i++){
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::all_group_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1037:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1037 | for (int i = 0; i < fn_.size(); i++) {
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1038:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1038 | for (int j = 0; j < fn_[i].size(); j++) {
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::all_log_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1048:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1048 | for (int i = 0; i < fn_.size(); i++) {
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1049:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1049 | for (int j = 0; j < fn_[i].size(); j++) {
| ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::any_log_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1061:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1061 | for(int i = 0; i < fn_.size(); i++){
| ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘strvec glmmr::Covariance::parameter_names()’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1212:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1212 | for(int i = 0; i < form_.re_.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~
In file included from ../inst/include/optim/optimclass.h:8,
from ../inst/include/glmmrOptim.h:6,
from gd_search.cpp:3:
../inst/include/optim/optimderivatives.h: In member function ‘void glmmr::OptimDerivatives::addDesign(glmmr::Covariance&, bool)’:
../inst/include/optim/optimderivatives.h:22:9: warning: unused variable ‘curr_size’ [-Wunused-variable]
22 | int curr_size = FirstOrderDerivatives.size();
| ^~~~~~~~~
../inst/include/optim/optimclass.h: In member function ‘Eigen::MatrixXd glmmr::OptimDesign::KR_correction(const Eigen::MatrixXd&, const int&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::ArrayXi&)’:
../inst/include/optim/optimclass.h:129:9: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<glmmr::MatrixField<Eigen::Matrix<double, -1, -1> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
129 | if(idx>=derivs_.FirstOrderDerivatives.size() )Rcpp::stop("idx out of range");
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:10:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h: In instantiation of ‘T glmmr::MatrixField<T>::operator()(int) const [with T = Eigen::Matrix<double, -1, -1>]’:
../inst/include/optim/optimclass.h:148:54: required from here
148 | partial1 = Z*derivs_.FirstOrderDerivatives[idx](i)*Z.transpose();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:38:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unique_ptr<Eigen::Matrix<double, -1, -1>, std::default_delete<Eigen::Matrix<double, -1, -1> > >, std::allocator<std::unique_ptr<Eigen::Matrix<double, -1, -1>, std::default_delete<Eigen::Matrix<double, -1, -1> > > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
38 | if(i >= data.size()) throw std::runtime_error("Accessing index out of range matrix field");
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h: In instantiation of ‘T glmmr::MatrixField<T>::operator()(int) const [with T = Eigen::Matrix<double, -1, 1>]’:
../inst/include/optim/optimclass.h:269:42: required from here
269 | vals(j) = c_obj_fun( M, data_.C_list_(j));
| ~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:38:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unique_ptr<Eigen::Matrix<double, -1, 1>, std::default_delete<Eigen::Matrix<double, -1, 1> > >, std::allocator<std::unique_ptr<Eigen::Matrix<double, -1, 1>, std::default_delete<Eigen::Matrix<double, -1, 1> > > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
38 | if(i >= data.size()) throw std::runtime_error("Accessing index out of range matrix field");
| ~~^~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:47,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:26:
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = glmmr::Covariance]’:
gd_search.cpp:155:25: required from here
155 | XPtr<glmmr::Covariance> mptr(mptr_);
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type ‘glmmr::Covariance’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o glmmrOptim.so RcppExports.o gd_search.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/glmmrOptim/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/glmmrOptim/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/glmmrOptim/src'
installing to /data/gannet/ripley/R/packages/tests-devel/glmmrOptim.Rcheck/00LOCK-glmmrOptim/00new/glmmrOptim/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (glmmrOptim)