* installing *source* package ‘glmmrOptim’ ...
** package ‘glmmrOptim’ 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/glmmrOptim/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'/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.h:3,
                 from ../inst/include/optim/optimderivatives.h:4,
                 from ../inst/include/optim/optimclass.h:8,
                 from ../inst/include/glmmrOptim.h:6,
                 from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:19: warning: "EIGEN_DEFAULT_DENSE_INDEX_TYPE" redefined
   19 | #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: 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/SparseChol/include/SparseChol.h:3,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:33:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In function 'int clear_flag(int, int, intvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable]
  145 |   int x ;
      |       ^
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::insert(int, int, double)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:342:18: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  342 |     if(Ap[row]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:349:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  349 |     for(int i = row+1; i < Ap.size(); i++)Ap[i]++;
      |                        ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:361:18: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  361 |     if(Ap[col]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:368:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  368 |     for(int i = col+1; i < Ap.size(); i++)Ap[i]++;
      |                        ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::transpose()':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:383:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  383 |   for (int i = 2; i < B.Ap.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'sparse& sparse::operator+=(const sparse&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable]
  415 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::AMD_order()':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable]
  625 |   double mem = 0;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable]
  626 |   int nz = Ap.back();
      |       ^~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable]
  815 |   int deg, inext, ilast;
      |                   ^~~~~
In file included from /data/gannet/ripley/R/test-dev/SparseChol/include/SparseChol.h:4:
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In function 'dblvec operator*(const sparse&, const dblvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:12:10: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   12 |   if(A.m != B.size())Rcpp::stop("wrong dimension in sparse-vector multiplication");
      |      ~~~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable]
   14 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In member function 'sparse& sparse::operator%=(const dblvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:37:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   37 |   for(int i = 0; i < Ax.size(); i++){
      |                  ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In function 'sparse SparseOperators::operator%(const sparse&, const Eigen::VectorXd&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:174:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
  174 |     for(unsigned int i = 0; i < A.m; i++){
      |                             ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h: In function 'bool glmmr::is_number(const std::string&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable]
  249 |     float a = std::stod(s);
      |           ^
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/formula.hpp:4,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:5:
/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:59:27: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   59 |   if(parameters_in.size() < parameter_count)Rcpp::stop("Expecting "+std::to_string(parameter_count)+" parameters in calculator but got "+std::to_string(parameters_in.size()));
      |      ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:61:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |   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:1333:30: 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]
 1333 |         if(indexes[idx_iter] >= parameter_names.size()){
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1348:30: 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]
 1348 |         if(indexes[idx_iter] >= data_names.size()){
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:6:
/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)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:167:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  167 |   for(int i = 0; i < formula.size(); i++)
      |                  ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable]
  208 |   bool add_check, variable_in_data;
      |                   ^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp: In member function 'void glmmr::Formula::tokenise()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:127:18: 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]
  127 |   for(int i =0; i<re_.size(); i++){
      |                 ~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:11,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/sparse.h: In function 'sparse glmmr::submat_sparse(const sparse&, intvec)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/sparse.h:24:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   24 |   for(int i = 0; i < rows.size(); i++){
      |                  ~~^~~~~~~~~~~~~
/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:183:22: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  183 |   if(colnames_.size()!= data_.cols())Rcpp::stop("colnames length != data columns");
      |      ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:256:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  256 |         for(k = 0; k < fnvars[idx].size(); k++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:270:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  270 |     for(j = 0; j< fnvars.size();j++){
      |                ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:271:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  271 |       for(k = 0; k < fnvars[j].size();k++){
      |                  ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:289:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  289 |     for(int m = 0; m < fnvars.size(); m++){
      |                    ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:291:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  291 |       for(int p = 0; p < fnvars[m].size(); p++){
      |                      ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:298:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  298 |     for(j = 0; j < groups.size(); j++){
      |                ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:313:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  313 |         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:339:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  339 |     for(int j = 0; j < fn_.size(); j++){
      |                    ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:345:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  345 |           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:346:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  346 |           for(int k = 0; k < fn_[j].size(); k++){
      |                          ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:370:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  370 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:371:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  371 |     for(int j = 0; j < re_pars_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:372:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  372 |       for(int k = 0; k < re_pars_[i][j].size(); k++){
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:380:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  380 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:387:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  387 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:391:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  391 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:414:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  414 |       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:420:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  420 |       for(int j = 0; j < (fn_[i].size()-1); j++){
      |                      ~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:434:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::calculator>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  434 |   for(int i = 0; i < calc_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:441:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::calculator>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  441 |   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 'virtual void glmmr::Covariance::update_parameters_extern(const dblvec&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:567:23: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  567 |   if(parameters.size()!=npar())Rcpp::stop(std::to_string(parameters.size())+" covariance parameters provided, "+std::to_string(npar())+" required");
      |      ~~~~~~~~~~~~~~~~~^~~~~~~~
/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:590:32: 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]
  590 |   } 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:973:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  973 |   for(int i = 0; i < fn_.size(); i++){
      |                  ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:974:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  974 |     for(int j = 0; j < fn_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~
/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:987:20: 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]
  987 |   for(int i = 0; i < form_.re_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:7:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp: In member function 'virtual void glmmr::LinearPredictor::update_parameters(const dblvec&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp:143:24: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  143 |   if(parameters_.size()!=P())Rcpp::stop(std::to_string(parameters_.size())+" parameters provided, "+std::to_string(P())+" required");
      |      ~~~~~~~~~~~~~~~~~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp:144:24: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  144 |   if(parameters_.size()!=calc.parameter_count)Rcpp::stop(std::to_string(parameters_.size())+" parameters provided, "+std::to_string(calc.parameter_count)+" required");
      |      ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelbits.hpp:5,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:4,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:8:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp: In member function 'void glmmr::hsgpCovariance::gen_indices()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:384:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  384 |   for(int i = 0; i < linspace_vec[0].size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:388:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  388 |   for(int i = 0; i < indices_vec.size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:389:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  389 |     for(int j = 0; j < indices_vec[0].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:5,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelbits.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/griddata.hpp: In member function 'Eigen::ArrayXi glmmr::griddata::top_i_pq(const Eigen::ArrayXd&, int)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/griddata.hpp:36:19: warning: comparison of integer expressions of different signedness: 'std::priority_queue<std::pair<double, int>, std::vector<std::pair<double, int> >, glmmr::griddata::top_i_pq(const Eigen::ArrayXd&, int)::ComparePair>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   36 |     if (pq.size() < n)
      |         ~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'virtual void glmmr::nngpCovariance::update_parameters(const Eigen::ArrayXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:250:32: 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]
  250 |   } else if(parameters_.size() == parameters.size()){
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'void glmmr::nngpCovariance::update_parameters_d(const Eigen::ArrayXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:266:32: 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]
  266 |   } else if(parameters_.size() == parameters.size()){
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'virtual Eigen::VectorXd glmmr::nngpCovariance::log_gradient(const Eigen::MatrixXd&, double&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable]
  381 |   double au, av, qf;
      |              ^~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:12,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:8:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::set_bounds(const Eigen::VectorXd&, const Eigen::VectorXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:431:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  431 |   for(int i = 0; i < dim; i++)
      |                  ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::set_bounds(const std::vector<double>&, const std::vector<double>&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:442:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  442 |   for(int i = 0; i < dim; i++)
      |                  ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::minimise()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable]
  503 |         double a = eval(current_values, g);
      |                ^
../inst/include/optim/optimderivatives.h: In member function 'void glmmr::OptimDerivatives::addDesign(glmmr::Covariance&, bool)':
../inst/include/optim/optimderivatives.h:20:9: warning: unused variable 'curr_size' [-Wunused-variable]
   20 |     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.h:4:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h: In instantiation of 'T glmmr::randomGaussian(T, Eigen::VectorXd&) [with T = boost::random::variate_generator<boost::random::mersenne_twister_engine<unsigned int, 32, 624, 397, 31, 2567483615, 11, 4294967295, 7, 2636928640, 15, 4022730752, 18, 1812433253>, boost::random::normal_distribution<> >; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:680:21:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h:15:24: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index' {aka 'long int'} [-Wsign-compare]
   15 |   for (size_t i = 0; i < res.size(); ++i)
      |                      ~~^~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h:3:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h: In instantiation of 'void glmmr::algo::combinations(const std::vector<std::vector<T> >&, int, int, std::vector<T>&, std::vector<std::vector<T> >&) [with T = int]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:385:30:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h:54:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   54 |   if(n == vecs.size()-1){
      |      ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h:57:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   57 |     for(int i = 0; i < vecs[n+1].size(); i++){
      |                    ~~^~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:46,
                 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::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:36:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   31 |     delete obj;
      |     ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:59:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:82:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   89 |   for(int i = 0; i< sigma_blocks.size(); i++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_algo.h:201,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:15:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_general.h: At global scope:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_general.h:251:1: warning: 'int bobyqa(long int, long int, double (*)(long int, const double*, void*), void*, double*, const double*, const double*, double, double, long int, long int, double*)' defined but not used [-Wunused-function]
  251 | bobyqa(const INTEGER n, const INTEGER npt,
      | ^~~~~~
In member function 'sparse& sparse::operator=(sparse)',
    inlined from 'void SparseChol::update(const sparse&)' at /data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h:64:21:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:271:9: warning: '<anonymous>.sparse::m' may be used uninitialized [-Wmaybe-uninitialized]
  271 |   m = B.m;
      |       ~~^
In file included from /data/gannet/ripley/R/test-dev/SparseChol/include/SparseChol.h:5:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h: In member function 'void SparseChol::update(const sparse&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h:64:21: note: '<anonymous>' declared here
   64 |       L = sparse(LAp);
      |                     ^
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'/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.h:3,
                 from gd_search.cpp:1:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:19: warning: "EIGEN_DEFAULT_DENSE_INDEX_TYPE" redefined
   19 | #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: 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/SparseChol/include/SparseChol.h:3,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:33:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In function 'int clear_flag(int, int, intvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable]
  145 |   int x ;
      |       ^
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::insert(int, int, double)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:342:18: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  342 |     if(Ap[row]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:349:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  349 |     for(int i = row+1; i < Ap.size(); i++)Ap[i]++;
      |                        ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:361:18: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  361 |     if(Ap[col]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:368:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  368 |     for(int i = col+1; i < Ap.size(); i++)Ap[i]++;
      |                        ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::transpose()':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:383:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  383 |   for (int i = 2; i < B.Ap.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'sparse& sparse::operator+=(const sparse&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable]
  415 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::AMD_order()':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable]
  625 |   double mem = 0;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable]
  626 |   int nz = Ap.back();
      |       ^~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable]
  815 |   int deg, inext, ilast;
      |                   ^~~~~
In file included from /data/gannet/ripley/R/test-dev/SparseChol/include/SparseChol.h:4:
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In function 'dblvec operator*(const sparse&, const dblvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:12:10: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   12 |   if(A.m != B.size())Rcpp::stop("wrong dimension in sparse-vector multiplication");
      |      ~~~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable]
   14 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In member function 'sparse& sparse::operator%=(const dblvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:37:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   37 |   for(int i = 0; i < Ax.size(); i++){
      |                  ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In function 'sparse SparseOperators::operator%(const sparse&, const Eigen::VectorXd&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:174:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
  174 |     for(unsigned int i = 0; i < A.m; i++){
      |                             ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h: In function 'bool glmmr::is_number(const std::string&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable]
  249 |     float a = std::stod(s);
      |           ^
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/formula.hpp:4,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:5:
/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:59:27: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   59 |   if(parameters_in.size() < parameter_count)Rcpp::stop("Expecting "+std::to_string(parameter_count)+" parameters in calculator but got "+std::to_string(parameters_in.size()));
      |      ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:61:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |   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:1333:30: 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]
 1333 |         if(indexes[idx_iter] >= parameter_names.size()){
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1348:30: 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]
 1348 |         if(indexes[idx_iter] >= data_names.size()){
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:6:
/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)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:167:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  167 |   for(int i = 0; i < formula.size(); i++)
      |                  ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable]
  208 |   bool add_check, variable_in_data;
      |                   ^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp: In member function 'void glmmr::Formula::tokenise()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:127:18: 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]
  127 |   for(int i =0; i<re_.size(); i++){
      |                 ~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:11,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/sparse.h: In function 'sparse glmmr::submat_sparse(const sparse&, intvec)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/sparse.h:24:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   24 |   for(int i = 0; i < rows.size(); i++){
      |                  ~~^~~~~~~~~~~~~
/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:183:22: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  183 |   if(colnames_.size()!= data_.cols())Rcpp::stop("colnames length != data columns");
      |      ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:256:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  256 |         for(k = 0; k < fnvars[idx].size(); k++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:270:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  270 |     for(j = 0; j< fnvars.size();j++){
      |                ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:271:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  271 |       for(k = 0; k < fnvars[j].size();k++){
      |                  ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:289:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  289 |     for(int m = 0; m < fnvars.size(); m++){
      |                    ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:291:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  291 |       for(int p = 0; p < fnvars[m].size(); p++){
      |                      ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:298:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  298 |     for(j = 0; j < groups.size(); j++){
      |                ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:313:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  313 |         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:339:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  339 |     for(int j = 0; j < fn_.size(); j++){
      |                    ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:345:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  345 |           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:346:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  346 |           for(int k = 0; k < fn_[j].size(); k++){
      |                          ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:370:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  370 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:371:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  371 |     for(int j = 0; j < re_pars_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:372:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  372 |       for(int k = 0; k < re_pars_[i][j].size(); k++){
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:380:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  380 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:387:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  387 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:391:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  391 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:414:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  414 |       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:420:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  420 |       for(int j = 0; j < (fn_[i].size()-1); j++){
      |                      ~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:434:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::calculator>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  434 |   for(int i = 0; i < calc_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:441:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::calculator>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  441 |   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 'virtual void glmmr::Covariance::update_parameters_extern(const dblvec&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:567:23: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  567 |   if(parameters.size()!=npar())Rcpp::stop(std::to_string(parameters.size())+" covariance parameters provided, "+std::to_string(npar())+" required");
      |      ~~~~~~~~~~~~~~~~~^~~~~~~~
/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:590:32: 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]
  590 |   } 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:973:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  973 |   for(int i = 0; i < fn_.size(); i++){
      |                  ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:974:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  974 |     for(int j = 0; j < fn_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~
/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:987:20: 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]
  987 |   for(int i = 0; i < form_.re_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:7:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp: In member function 'virtual void glmmr::LinearPredictor::update_parameters(const dblvec&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp:143:24: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  143 |   if(parameters_.size()!=P())Rcpp::stop(std::to_string(parameters_.size())+" parameters provided, "+std::to_string(P())+" required");
      |      ~~~~~~~~~~~~~~~~~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp:144:24: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  144 |   if(parameters_.size()!=calc.parameter_count)Rcpp::stop(std::to_string(parameters_.size())+" parameters provided, "+std::to_string(calc.parameter_count)+" required");
      |      ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelbits.hpp:5,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:4,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:8:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp: In member function 'void glmmr::hsgpCovariance::gen_indices()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:384:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  384 |   for(int i = 0; i < linspace_vec[0].size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:388:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  388 |   for(int i = 0; i < indices_vec.size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:389:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  389 |     for(int j = 0; j < indices_vec[0].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:5,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelbits.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/griddata.hpp: In member function 'Eigen::ArrayXi glmmr::griddata::top_i_pq(const Eigen::ArrayXd&, int)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/griddata.hpp:36:19: warning: comparison of integer expressions of different signedness: 'std::priority_queue<std::pair<double, int>, std::vector<std::pair<double, int> >, glmmr::griddata::top_i_pq(const Eigen::ArrayXd&, int)::ComparePair>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   36 |     if (pq.size() < n)
      |         ~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'virtual void glmmr::nngpCovariance::update_parameters(const Eigen::ArrayXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:250:32: 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]
  250 |   } else if(parameters_.size() == parameters.size()){
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'void glmmr::nngpCovariance::update_parameters_d(const Eigen::ArrayXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:266:32: 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]
  266 |   } else if(parameters_.size() == parameters.size()){
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'virtual Eigen::VectorXd glmmr::nngpCovariance::log_gradient(const Eigen::MatrixXd&, double&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable]
  381 |   double au, av, qf;
      |              ^~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:12,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:8:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::set_bounds(const Eigen::VectorXd&, const Eigen::VectorXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:431:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  431 |   for(int i = 0; i < dim; i++)
      |                  ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::set_bounds(const std::vector<double>&, const std::vector<double>&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:442:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  442 |   for(int i = 0; i < dim; i++)
      |                  ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::minimise()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable]
  503 |         double a = eval(current_values, g);
      |                ^
In file included from ../inst/include/optim/optimclass.h:8,
                 from ../inst/include/glmmrOptim.h:6,
                 from gd_search.cpp:2:
../inst/include/optim/optimderivatives.h: In member function 'void glmmr::OptimDerivatives::addDesign(glmmr::Covariance&, bool)':
../inst/include/optim/optimderivatives.h:20:9: warning: unused variable 'curr_size' [-Wunused-variable]
   20 |     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.h:4:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h: In instantiation of 'T glmmr::randomGaussian(T, Eigen::VectorXd&) [with T = boost::random::variate_generator<boost::random::mersenne_twister_engine<unsigned int, 32, 624, 397, 31, 2567483615, 11, 4294967295, 7, 2636928640, 15, 4022730752, 18, 1812433253>, boost::random::normal_distribution<> >; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:680:21:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h:15:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index' {aka 'long int'} [-Wsign-compare]
   15 |   for (size_t i = 0; i < res.size(); ++i)
      |                      ~~^~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h:3:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h: In instantiation of 'void glmmr::algo::combinations(const std::vector<std::vector<T> >&, int, int, std::vector<T>&, std::vector<std::vector<T> >&) [with T = int]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:385:30:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h:54:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   54 |   if(n == vecs.size()-1){
      |      ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h:57:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   57 |     for(int i = 0; i < vecs[n+1].size(); i++){
      |                    ~~^~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:46,
                 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::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:36:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   31 |     delete obj;
      |     ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:59:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:82:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
/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:123:25:   required from here
/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]
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   89 |   for(int i = 0; i< sigma_blocks.size(); i++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_algo.h:201,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:15:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_general.h: At global scope:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_general.h:251:1: warning: 'int bobyqa(long int, long int, double (*)(long int, const double*, void*), void*, double*, const double*, const double*, double, double, long int, long int, double*)' defined but not used [-Wunused-function]
  251 | bobyqa(const INTEGER n, const INTEGER npt,
      | ^~~~~~
In member function 'sparse& sparse::operator=(sparse)',
    inlined from 'void SparseChol::update(const sparse&)' at /data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h:64:21:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:271:9: warning: '<anonymous>.sparse::m' may be used uninitialized [-Wmaybe-uninitialized]
  271 |   m = B.m;
      |       ~~^
In file included from /data/gannet/ripley/R/test-dev/SparseChol/include/SparseChol.h:5:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h: In member function 'void SparseChol::update(const sparse&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h:64:21: note: '<anonymous>' declared here
   64 |       L = sparse(LAp);
      |                     ^
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'/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 openmp_utils.cpp -o openmp_utils.o
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:3,
                 from ../inst/include/optim/optimderivatives.h:4,
                 from ../inst/include/optim/optimclass.h:8,
                 from ../inst/include/glmmrOptim.h:6,
                 from openmp_utils.cpp:2:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:19: warning: "EIGEN_DEFAULT_DENSE_INDEX_TYPE" redefined
   19 | #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: 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/SparseChol/include/SparseChol.h:3,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:33:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In function 'int clear_flag(int, int, intvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable]
  145 |   int x ;
      |       ^
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::insert(int, int, double)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:342:18: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  342 |     if(Ap[row]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:349:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  349 |     for(int i = row+1; i < Ap.size(); i++)Ap[i]++;
      |                        ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:361:18: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  361 |     if(Ap[col]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:368:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  368 |     for(int i = col+1; i < Ap.size(); i++)Ap[i]++;
      |                        ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::transpose()':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:383:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  383 |   for (int i = 2; i < B.Ap.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'sparse& sparse::operator+=(const sparse&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable]
  415 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h: In member function 'void sparse::AMD_order()':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable]
  625 |   double mem = 0;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable]
  626 |   int nz = Ap.back();
      |       ^~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable]
  815 |   int deg, inext, ilast;
      |                   ^~~~~
In file included from /data/gannet/ripley/R/test-dev/SparseChol/include/SparseChol.h:4:
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In function 'dblvec operator*(const sparse&, const dblvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:12:10: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   12 |   if(A.m != B.size())Rcpp::stop("wrong dimension in sparse-vector multiplication");
      |      ~~~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable]
   14 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In member function 'sparse& sparse::operator%=(const dblvec&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:37:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   37 |   for(int i = 0; i < Ax.size(); i++){
      |                  ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h: In function 'sparse SparseOperators::operator%(const sparse&, const Eigen::VectorXd&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/operators.h:174:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
  174 |     for(unsigned int i = 0; i < A.m; i++){
      |                             ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h: In function 'bool glmmr::is_number(const std::string&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable]
  249 |     float a = std::stod(s);
      |           ^
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/formula.hpp:4,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:5:
/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:59:27: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   59 |   if(parameters_in.size() < parameter_count)Rcpp::stop("Expecting "+std::to_string(parameter_count)+" parameters in calculator but got "+std::to_string(parameters_in.size()));
      |      ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:61:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |   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:1333:30: 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]
 1333 |         if(indexes[idx_iter] >= parameter_names.size()){
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1348:30: 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]
 1348 |         if(indexes[idx_iter] >= data_names.size()){
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:6:
/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)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:167:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  167 |   for(int i = 0; i < formula.size(); i++)
      |                  ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable]
  208 |   bool add_check, variable_in_data;
      |                   ^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp: In member function 'void glmmr::Formula::tokenise()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:127:18: 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]
  127 |   for(int i =0; i<re_.size(); i++){
      |                 ~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:11,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/sparse.h: In function 'sparse glmmr::submat_sparse(const sparse&, intvec)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/sparse.h:24:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   24 |   for(int i = 0; i < rows.size(); i++){
      |                  ~~^~~~~~~~~~~~~
/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:183:22: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  183 |   if(colnames_.size()!= data_.cols())Rcpp::stop("colnames length != data columns");
      |      ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:256:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  256 |         for(k = 0; k < fnvars[idx].size(); k++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:270:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  270 |     for(j = 0; j< fnvars.size();j++){
      |                ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:271:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  271 |       for(k = 0; k < fnvars[j].size();k++){
      |                  ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:289:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  289 |     for(int m = 0; m < fnvars.size(); m++){
      |                    ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:291:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  291 |       for(int p = 0; p < fnvars[m].size(); p++){
      |                      ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:298:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  298 |     for(j = 0; j < groups.size(); j++){
      |                ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:313:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  313 |         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:339:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  339 |     for(int j = 0; j < fn_.size(); j++){
      |                    ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:345:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  345 |           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:346:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  346 |           for(int k = 0; k < fn_[j].size(); k++){
      |                          ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:370:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  370 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:371:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  371 |     for(int j = 0; j < re_pars_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:372:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  372 |       for(int k = 0; k < re_pars_[i][j].size(); k++){
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:380:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  380 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:387:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  387 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:391:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  391 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:414:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  414 |       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:420:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  420 |       for(int j = 0; j < (fn_[i].size()-1); j++){
      |                      ~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:434:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::calculator>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  434 |   for(int i = 0; i < calc_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:441:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::calculator>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  441 |   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 'virtual void glmmr::Covariance::update_parameters_extern(const dblvec&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:567:23: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  567 |   if(parameters.size()!=npar())Rcpp::stop(std::to_string(parameters.size())+" covariance parameters provided, "+std::to_string(npar())+" required");
      |      ~~~~~~~~~~~~~~~~~^~~~~~~~
/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:590:32: 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]
  590 |   } 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:973:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<glmmr::CovFunc> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  973 |   for(int i = 0; i < fn_.size(); i++){
      |                  ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:974:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::CovFunc>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  974 |     for(int j = 0; j < fn_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~
/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:987:20: 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]
  987 |   for(int i = 0; i < form_.re_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:7:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp: In member function 'virtual void glmmr::LinearPredictor::update_parameters(const dblvec&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp:143:24: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  143 |   if(parameters_.size()!=P())Rcpp::stop(std::to_string(parameters_.size())+" parameters provided, "+std::to_string(P())+" required");
      |      ~~~~~~~~~~~~~~~~~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/linearpredictor.hpp:144:24: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  144 |   if(parameters_.size()!=calc.parameter_count)Rcpp::stop(std::to_string(parameters_.size())+" parameters provided, "+std::to_string(calc.parameter_count)+" required");
      |      ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelbits.hpp:5,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:4,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:8:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp: In member function 'void glmmr::hsgpCovariance::gen_indices()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:384:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  384 |   for(int i = 0; i < linspace_vec[0].size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:388:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  388 |   for(int i = 0; i < indices_vec.size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:389:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  389 |     for(int j = 0; j < indices_vec[0].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:5,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelbits.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/griddata.hpp: In member function 'Eigen::ArrayXi glmmr::griddata::top_i_pq(const Eigen::ArrayXd&, int)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/griddata.hpp:36:19: warning: comparison of integer expressions of different signedness: 'std::priority_queue<std::pair<double, int>, std::vector<std::pair<double, int> >, glmmr::griddata::top_i_pq(const Eigen::ArrayXd&, int)::ComparePair>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   36 |     if (pq.size() < n)
      |         ~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'virtual void glmmr::nngpCovariance::update_parameters(const Eigen::ArrayXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:250:32: 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]
  250 |   } else if(parameters_.size() == parameters.size()){
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'void glmmr::nngpCovariance::update_parameters_d(const Eigen::ArrayXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:266:32: 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]
  266 |   } else if(parameters_.size() == parameters.size()){
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp: In member function 'virtual Eigen::VectorXd glmmr::nngpCovariance::log_gradient(const Eigen::MatrixXd&, double&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable]
  381 |   double au, av, qf;
      |              ^~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:12,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:8:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::set_bounds(const Eigen::VectorXd&, const Eigen::VectorXd&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:431:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  431 |   for(int i = 0; i < dim; i++)
      |                  ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::set_bounds(const std::vector<double>&, const std::vector<double>&)':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:442:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  442 |   for(int i = 0; i < dim; i++)
      |                  ~~^~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h: In member function 'void optim<double(const Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&), LBFGS>::minimise()':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable]
  503 |         double a = eval(current_values, g);
      |                ^
../inst/include/optim/optimderivatives.h: In member function 'void glmmr::OptimDerivatives::addDesign(glmmr::Covariance&, bool)':
../inst/include/optim/optimderivatives.h:20:9: warning: unused variable 'curr_size' [-Wunused-variable]
   20 |     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.h:4:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h: In instantiation of 'T glmmr::randomGaussian(T, Eigen::VectorXd&) [with T = boost::random::variate_generator<boost::random::mersenne_twister_engine<unsigned int, 32, 624, 397, 31, 2567483615, 11, 4294967295, 7, 2636928640, 15, 4022730752, 18, 1812433253>, boost::random::normal_distribution<> >; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:680:21:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h:15:24: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index' {aka 'long int'} [-Wsign-compare]
   15 |   for (size_t i = 0; i < res.size(); ++i)
      |                      ~~^~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h:3:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h: In instantiation of 'void glmmr::algo::combinations(const std::vector<std::vector<T> >&, int, int, std::vector<T>&, std::vector<std::vector<T> >&) [with T = int]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/hsgpcovariance.hpp:385:30:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h:54:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   54 |   if(n == vecs.size()-1){
      |      ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/algo.h:57:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   57 |     for(int i = 0; i < vecs[n+1].size(); i++){
      |                    ~~^~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:46,
                 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::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:36:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   31 |     delete obj;
      |     ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:59:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor> >]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr.h:31:82:   required from here
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor> >' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp: In instantiation of 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:206:60: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  206 |    if(re_type == RandomEffectMargin::At && atrevals.size() != model.covariance.Q())Rcpp::stop("Need to provide values for u vector");
      |                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:229:22: 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]
  229 |     for(int p = 0; p < at.size(); p++){
      |                    ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:244:22: 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]
  244 |     for(int p = 0; p < atmeans.size(); p++){
      |                    ~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'void glmmr::ModelOptim<modeltype>::update_beta(const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblvec = std::vector<double>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:61:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:826:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  826 |     for(int i = 0; i < beta.size(); i++)
      |                    ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp: In instantiation of 'Eigen::ArrayXd glmmr::ModelOptim<modeltype>::optimum_weights(double, Eigen::VectorXd, double, int) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; Eigen::ArrayXd = Eigen::Array<double, -1, 1>; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:87:19:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1262:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1262 |       for(int i = 0 ; i < SB.size(); i++){
      |                       ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1284:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1284 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1308:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Eigen::Matrix<double, -1, -1> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1308 |           for(int k = 0; k < Xs.size(); k++){
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1319:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1319 |       for(int k = 0; k < SB.size(); k++){
      |                      ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modeloptim.hpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1326 |     for(int i = 0 ; i < SB.size(); i++){
      |                     ~~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   89 |   for(int i = 0; i< sigma_blocks.size(); i++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp: In instantiation of 'Eigen::MatrixXd glmmr::ModelMatrix<modeltype>::information_matrix() [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]':
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:299:36:   required from 'dblpair glmmr::Model<modeltype>::marginal(glmmr::MarginType, const std::string&, const strvec&, const strvec&, const strvec&, glmmr::RandomEffectMargin, glmmr::SE, const dblpair&, const dblvec&, const dblvec&) [with modeltype = glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>; dblpair = std::pair<double, double>; std::string = std::__cxx11::basic_string<char>; strvec = std::vector<std::__cxx11::basic_string<char> >; dblvec = std::vector<double>]'
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/model.hpp:169:16:   required from here
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/modelmatrix.hpp:89:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<glmmr::SigmaBlock>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_algo.h:201,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/optim.h:15:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_general.h: At global scope:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/optim/bobyqa_general.h:251:1: warning: 'int bobyqa(long int, long int, double (*)(long int, const double*, void*), void*, double*, const double*, const double*, double, double, long int, long int, double*)' defined but not used [-Wunused-function]
  251 | bobyqa(const INTEGER n, const INTEGER npt,
      | ^~~~~~
In member function 'sparse& sparse::operator=(sparse)',
    inlined from 'void SparseChol::update(const sparse&)' at /data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h:64:21:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:271:9: warning: '<anonymous>.sparse::m' may be used uninitialized [-Wmaybe-uninitialized]
  271 |   m = B.m;
      |       ~~^
In file included from /data/gannet/ripley/R/test-dev/SparseChol/include/SparseChol.h:5:
/data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h: In member function 'void SparseChol::update(const sparse&)':
/data/gannet/ripley/R/test-dev/SparseChol/include/sparseldl.h:64:21: note: '<anonymous>' declared here
   64 |       L = sparse(LAp);
      |                     ^
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 glmmrOptim.so RcppExports.o gd_search.o openmp_utils.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)