* installing *source* package ‘glmmrOptim’ ...
** this is package ‘glmmrOptim’ version ‘0.3.6’
** package ‘glmmrOptim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/glmmrOptim/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/glmmrBase/include' -I'/data/gannet/ripley/R/test-dev/SparseChol/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/rminqa/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:4,
                 from ../inst/include/optim/optimdata.h:4,
                 from ../inst/include/optim/optimclass.h:7,
                 from ../inst/include/glmmrOptim.h:6,
                 from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:21:9: warning: ‘EIGEN_DEFAULT_DENSE_INDEX_TYPE’ redefined
   21 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:19,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Dense:1,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigenForward.h:28,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
                 from ../inst/include/glmmrOptim.h:4:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: this is the location of the previous definition
   33 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/optim/optimderivatives.h:4,
                 from ../inst/include/optim/optimclass.h:8:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1059:1: warning: multi-line comment [-Wcomment]
 1059 | //#pragma omp declare reduction(vec_dbl_plus : std::vector<double> : \
      | ^
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:39:
/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:353:20: 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]
  353 |       if(Ap[row]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:360:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  360 |       for(int i = row+1; i < Ap.size(); i++)Ap[i]++;
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:382:20: 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]
  382 |       if(Ap[col]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:389:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  389 |       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:405:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  405 |   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:437:10: warning: unused variable ‘val’ [-Wunused-variable]
  437 |   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:647:10: warning: unused variable ‘mem’ [-Wunused-variable]
  647 |   double mem = 0;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:648:7: warning: unused variable ‘nz’ [-Wunused-variable]
  648 |   int nz = Ap.back();
      |       ^~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:837:19: warning: unused variable ‘ilast’ [-Wunused-variable]
  837 |   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++){
      |                             ~~^~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/interpreter.h:4,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp: In member function ‘void glmmr::calculator::update_parameters(const dblvec&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:64:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   64 |   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:1336:30: 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]
 1336 |         if(indexes[idx_iter] >= parameter_names.size()){
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1351:30: 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]
 1351 |         if(indexes[idx_iter] >= data_names.size()){
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:6,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:7:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h: In function ‘bool glmmr::is_number(const std::string&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:12:11: warning: unused variable ‘a’ [-Wunused-variable]
   12 |     float a = std::stod(s);
      |           ^
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h: In function ‘void glmmr::two_way_fn(std::vector<char>&, calculator&, const Eigen::ArrayXXd&, const strvec&, Eigen::MatrixXd&, int, bool)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:223:19: warning: variable ‘variable_in_data’ set but not used [-Wunused-but-set-variable]
  223 |   bool add_check, variable_in_data;
      |                   ^~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:8:
/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:282:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  282 |         for(k = 0; k < fnvars[idx].size(); k++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:296:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  296 |     for(j = 0; j< fnvars.size();j++){
      |                ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:297:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  297 |       for(k = 0; k < fnvars[j].size();k++){
      |                  ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:315:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  315 |     for(int m = 0; m < fnvars.size(); m++){
      |                    ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  317 |       for(int p = 0; p < fnvars[m].size(); p++){
      |                      ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:324:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  324 |     for(j = 0; j < groups.size(); j++){
      |                ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:337:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  337 |         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:363:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  363 |     for(int j = 0; j < fn_.size(); j++){
      |                    ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:369:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  369 |           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:370:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  370 |           for(int k = 0; k < fn_[j].size(); k++){
      |                          ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:394:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  394 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:395:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |     for(int j = 0; j < re_pars_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:396:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  396 |       for(int k = 0; k < re_pars_[i][j].size(); k++){
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:404:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  404 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:411:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  411 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:415:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  415 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:438:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  438 |       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:444:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  444 |       for(int j = 0; j < (fn_[i].size()-1); j++){
      |                      ~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:458:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::calculator>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  458 |   for(int i = 0; i < calc_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:465:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::calculator>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  465 |   for(int i = 0; i < calc_.size(); i++) re_count_[re_order_[i]] += re_temp_data_[i].size();
      |                  ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘void glmmr::Covariance::Z_updater()’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:525:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::ZNonZero>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  525 |     for(int i = 0; i < z_nonzero.size(); i++){
      |                    ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:526:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  526 |       for(int j = 0; j < z_nonzero[i].rows.size(); j++){
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘virtual void glmmr::Covariance::update_parameters(const Eigen::ArrayXd&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:642:32: 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]
  642 |   } 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:1022:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1022 |   for(int i = 0; i < fn_.size(); i++){
      |                  ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1023:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1023 |     for(int j = 0; j < fn_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::all_group_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1036:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1036 |     for (int i = 0; i < fn_.size(); i++) {
      |                     ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1037:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1037 |         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:1046:20: 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]
 1046 |   for(int i = 0; i < form_.re_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~
../inst/include/optim/optimderivatives.h: In member function ‘void glmmr::OptimDerivatives::addDesign(glmmr::Covariance&, bool)’:
../inst/include/optim/optimderivatives.h:22:9: warning: unused variable ‘curr_size’ [-Wunused-variable]
   22 |     int curr_size = FirstOrderDerivatives.size();
      |         ^~~~~~~~~
../inst/include/optim/optimclass.h: In member function ‘Eigen::MatrixXd glmmr::OptimDesign::KR_correction(const Eigen::MatrixXd&, const int&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::ArrayXi&)’:
../inst/include/optim/optimclass.h:129:9: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<glmmr::MatrixField<Eigen::Matrix<double, -1, -1> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  129 |   if(idx>=derivs_.FirstOrderDerivatives.size() )Rcpp::stop("idx out of range");
      |      ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h: In instantiation of ‘T glmmr::MatrixField<T>::operator()(int) const [with T = Eigen::Matrix<double, -1, -1>]’:
../inst/include/optim/optimclass.h:148:54:   required from here
  148 |       partial1 = Z*derivs_.FirstOrderDerivatives[idx](i)*Z.transpose();
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:38:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unique_ptr<Eigen::Matrix<double, -1, -1>, std::default_delete<Eigen::Matrix<double, -1, -1> > >, std::allocator<std::unique_ptr<Eigen::Matrix<double, -1, -1>, std::default_delete<Eigen::Matrix<double, -1, -1> > > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   38 |     if(i >= data.size()) throw std::runtime_error("Accessing index out of range matrix field");
      |        ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h: In instantiation of ‘T glmmr::MatrixField<T>::operator()(int) const [with T = Eigen::Matrix<double, -1, 1>]’:
../inst/include/optim/optimclass.h:269:42:   required from here
  269 |     vals(j) = c_obj_fun( M, data_.C_list_(j));
      |                             ~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:38:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unique_ptr<Eigen::Matrix<double, -1, 1>, std::default_delete<Eigen::Matrix<double, -1, 1> > >, std::allocator<std::unique_ptr<Eigen::Matrix<double, -1, 1>, std::default_delete<Eigen::Matrix<double, -1, 1> > > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   38 |     if(i >= data.size()) throw std::runtime_error("Accessing index out of range matrix field");
      |        ~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/glmmrBase/include' -I'/data/gannet/ripley/R/test-dev/SparseChol/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/rminqa/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c gd_search.cpp -o gd_search.o
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/maths.h:6,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:5,
                 from gd_search.cpp:1:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:21:9: warning: ‘EIGEN_DEFAULT_DENSE_INDEX_TYPE’ redefined
   21 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:19,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Dense:1,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigenForward.h:28,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/general.h:10:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: this is the location of the previous definition
   33 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1059:1: warning: multi-line comment [-Wcomment]
 1059 | //#pragma omp declare reduction(vec_dbl_plus : std::vector<double> : \
      | ^
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:39:
/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:353:20: 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]
  353 |       if(Ap[row]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:360:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  360 |       for(int i = row+1; i < Ap.size(); i++)Ap[i]++;
      |                          ~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:382:20: 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]
  382 |       if(Ap[col]+p >= Ai.size()){
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:389:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  389 |       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:405:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  405 |   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:437:10: warning: unused variable ‘val’ [-Wunused-variable]
  437 |   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:647:10: warning: unused variable ‘mem’ [-Wunused-variable]
  647 |   double mem = 0;
      |          ^~~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:648:7: warning: unused variable ‘nz’ [-Wunused-variable]
  648 |   int nz = Ap.back();
      |       ^~
/data/gannet/ripley/R/test-dev/SparseChol/include/sparsematrix.h:837:19: warning: unused variable ‘ilast’ [-Wunused-variable]
  837 |   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++){
      |                             ~~^~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/interpreter.h:4,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:6:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp: In member function ‘void glmmr::calculator::update_parameters(const dblvec&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:64:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   64 |   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:1336:30: 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]
 1336 |         if(indexes[idx_iter] >= parameter_names.size()){
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:1351:30: 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]
 1351 |         if(indexes[idx_iter] >= data_names.size()){
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formula.hpp:6,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:7:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h: In function ‘bool glmmr::is_number(const std::string&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:12:11: warning: unused variable ‘a’ [-Wunused-variable]
   12 |     float a = std::stod(s);
      |           ^
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h: In function ‘void glmmr::two_way_fn(std::vector<char>&, calculator&, const Eigen::ArrayXXd&, const strvec&, Eigen::MatrixXd&, int, bool)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/formulaparse.h:223:19: warning: variable ‘variable_in_data’ set but not used [-Wunused-but-set-variable]
  223 |   bool add_check, variable_in_data;
      |                   ^~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:8:
/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:282:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  282 |         for(k = 0; k < fnvars[idx].size(); k++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:296:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  296 |     for(j = 0; j< fnvars.size();j++){
      |                ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:297:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  297 |       for(k = 0; k < fnvars[j].size();k++){
      |                  ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:315:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  315 |     for(int m = 0; m < fnvars.size(); m++){
      |                    ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  317 |       for(int p = 0; p < fnvars[m].size(); p++){
      |                      ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:324:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  324 |     for(j = 0; j < groups.size(); j++){
      |                ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:337:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  337 |         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:363:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  363 |     for(int j = 0; j < fn_.size(); j++){
      |                    ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:369:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  369 |           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:370:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  370 |           for(int k = 0; k < fn_[j].size(); k++){
      |                          ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:394:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  394 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:395:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |     for(int j = 0; j < re_pars_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:396:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  396 |       for(int k = 0; k < re_pars_[i][j].size(); k++){
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:404:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  404 |   for(int i =0; i<fn_.size();i++){
      |                 ~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:411:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  411 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:415:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  415 |     for(int j = 0; j<fn_[i].size();j++){
      |                    ~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:438:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  438 |       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:444:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  444 |       for(int j = 0; j < (fn_[i].size()-1); j++){
      |                      ~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:458:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::calculator>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  458 |   for(int i = 0; i < calc_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:465:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::calculator>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  465 |   for(int i = 0; i < calc_.size(); i++) re_count_[re_order_[i]] += re_temp_data_[i].size();
      |                  ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘void glmmr::Covariance::Z_updater()’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:525:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::ZNonZero>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  525 |     for(int i = 0; i < z_nonzero.size(); i++){
      |                    ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:526:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  526 |       for(int j = 0; j < z_nonzero[i].rows.size(); j++){
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘virtual void glmmr::Covariance::update_parameters(const Eigen::ArrayXd&)’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:642:32: 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]
  642 |   } 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:1022:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1022 |   for(int i = 0; i < fn_.size(); i++){
      |                  ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1023:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1023 |     for(int j = 0; j < fn_[i].size(); j++){
      |                    ~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp: In member function ‘bool glmmr::Covariance::all_group_re() const’:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1036:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<glmmr::CovFunc> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1036 |     for (int i = 0; i < fn_.size(); i++) {
      |                     ~~^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/covariance.hpp:1037:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<glmmr::CovFunc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1037 |         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:1046:20: 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]
 1046 |   for(int i = 0; i < form_.re_.size(); i++){
      |                  ~~^~~~~~~~~~~~~~~~~~
In file included from ../inst/include/optim/optimclass.h:8,
                 from ../inst/include/glmmrOptim.h:6,
                 from gd_search.cpp:3:
../inst/include/optim/optimderivatives.h: In member function ‘void glmmr::OptimDerivatives::addDesign(glmmr::Covariance&, bool)’:
../inst/include/optim/optimderivatives.h:22:9: warning: unused variable ‘curr_size’ [-Wunused-variable]
   22 |     int curr_size = FirstOrderDerivatives.size();
      |         ^~~~~~~~~
../inst/include/optim/optimclass.h: In member function ‘Eigen::MatrixXd glmmr::OptimDesign::KR_correction(const Eigen::MatrixXd&, const int&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::ArrayXi&)’:
../inst/include/optim/optimclass.h:129:9: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<glmmr::MatrixField<Eigen::Matrix<double, -1, -1> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  129 |   if(idx>=derivs_.FirstOrderDerivatives.size() )Rcpp::stop("idx out of range");
      |      ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/optim/optimdata.h:4,
                 from ../inst/include/optim/optimclass.h:7:
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h: In instantiation of ‘T glmmr::MatrixField<T>::operator()(int) const [with T = Eigen::Matrix<double, -1, -1>]’:
../inst/include/optim/optimclass.h:148:54:   required from here
  148 |       partial1 = Z*derivs_.FirstOrderDerivatives[idx](i)*Z.transpose();
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:38:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unique_ptr<Eigen::Matrix<double, -1, -1>, std::default_delete<Eigen::Matrix<double, -1, -1> > >, std::allocator<std::unique_ptr<Eigen::Matrix<double, -1, -1>, std::default_delete<Eigen::Matrix<double, -1, -1> > > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   38 |     if(i >= data.size()) throw std::runtime_error("Accessing index out of range matrix field");
      |        ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h: In instantiation of ‘T glmmr::MatrixField<T>::operator()(int) const [with T = Eigen::Matrix<double, -1, 1>]’:
../inst/include/optim/optimclass.h:269:42:   required from here
  269 |     vals(j) = c_obj_fun( M, data_.C_list_(j));
      |                             ~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/matrixfield.h:38:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unique_ptr<Eigen::Matrix<double, -1, 1>, std::default_delete<Eigen::Matrix<double, -1, 1> > >, std::allocator<std::unique_ptr<Eigen::Matrix<double, -1, 1>, std::default_delete<Eigen::Matrix<double, -1, 1> > > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   38 |     if(i >= data.size()) throw std::runtime_error("Accessing index out of range matrix field");
      |        ~~^~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:47,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:26:
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = glmmr::Covariance]’:
gd_search.cpp:155:25:   required from here
  155 |   XPtr<glmmr::Covariance> mptr(mptr_);
      |                         ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type ‘glmmr::Covariance’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   31 |     delete obj;
      |     ^~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/bessel.hpp:30,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:4:
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp: In function ‘int boost::math::detail::bessel_ik(T, T, T*, T*, int, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:421:22: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
  421 |         T z = (u + n % 2);
      |                    ~~^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:311:14: note: ‘n’ was declared here
  311 |     unsigned n, k;
      |              ^
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:421:11: warning: ‘u’ may be used uninitialized [-Wmaybe-uninitialized]
  421 |         T z = (u + n % 2);
      |           ^
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:308:7: note: ‘u’ was declared here
  308 |     T u, Iv, Kv, Kv1, Ku, Ku1, fv;
      |       ^
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/bessel.hpp:30,
                 from /data/gannet/ripley/R/test-dev/glmmrBase/include/glmmr/calculator.hpp:4:
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp: In function ‘int boost::math::detail::bessel_ik(T, T, T*, T*, int, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:421:22: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
  421 |         T z = (u + n % 2);
      |                    ~~^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:311:14: note: ‘n’ was declared here
  311 |     unsigned n, k;
      |              ^
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:421:11: warning: ‘u’ may be used uninitialized [-Wmaybe-uninitialized]
  421 |         T z = (u + n % 2);
      |           ^
/data/gannet/ripley/R/test-dev/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:308:7: note: ‘u’ was declared here
  308 |     T u, Iv, Kv, Kv1, Ku, Ku1, fv;
      |       ^
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o glmmrOptim.so RcppExports.o gd_search.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/glmmrOptim/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/glmmrOptim/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/glmmrOptim/src'
installing to /data/gannet/ripley/R/packages/tests-devel/glmmrOptim.Rcheck/00LOCK-glmmrOptim/00new/glmmrOptim/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (glmmrOptim)