* installing *source* package ‘glmmrOptim’ ...
** package ‘glmmrOptim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.4’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/glmmrOptim/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/glmmrBase/include' -I'/data/gannet/ripley/R/test-clang/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/rminqa/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -fopenmp  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:19:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined]
   19 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
      |         ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here
   33 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
      |         ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:33:
In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3:
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable]
  145 |   int x ;
      |       ^
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable]
  415 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable]
  625 |   double mem = 0;
      |          ^~~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable]
  626 |   int nz = Ap.back();
      |       ^~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable]
  787 |   int ncmpa = 0 ;
      |       ^
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable]
  815 |   int deg, inext, ilast;
      |                   ^~~~~
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:33:
In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4:
/data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable]
   14 |   double val;
      |          ^~~
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable]
  249 |     float a = std::stod(s);
      |           ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:5:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/formula.hpp:6:
/data/gannet/ripley/R/test-clang/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;
      |                   ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modelbits.hpp:6:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable]
  381 |   double au, av, qf;
      |              ^~
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:354:12: warning: unused variable 'result' [-Wunused-variable]
  354 |     double result = newuoa_closure( &closure, dim, control.npt, current_values.data(), control.rhobeg, control.rhoend, control.maxfun, w.data(), &fn_counter);
      |            ^~~~~~
/data/gannet/ripley/R/test-clang/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 RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
./../inst/include/optim/optimderivatives.h:20:9: warning: unused variable 'curr_size' [-Wunused-variable]
   20 |     int curr_size = FirstOrderDerivatives.size();
      |         ^~~~~~~~~
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:26:
In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:46:
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:15:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/bobyqa_algo.h:201:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/bobyqa_general.h:251:1: warning: unused function 'bobyqa' [-Wunused-function]
  251 | bobyqa(const INTEGER n, const INTEGER npt,
      | ^~~~~~
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/glmmrOptim.h:6:
In file included from ./../inst/include/optim/optimclass.h:8:
In file included from ./../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field]
  413 |   int              iter = 0;
      |                    ^
24 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/glmmrBase/include' -I'/data/gannet/ripley/R/test-clang/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/rminqa/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -fopenmp  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c gd_search.cpp -o gd_search.o
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:10:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:10:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:10:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:10:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:19:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined]
   19 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
      |         ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here
   33 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
      |         ^
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:33:
In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3:
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable]
  145 |   int x ;
      |       ^
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable]
  415 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable]
  625 |   double mem = 0;
      |          ^~~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable]
  626 |   int nz = Ap.back();
      |       ^~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable]
  787 |   int ncmpa = 0 ;
      |       ^
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable]
  815 |   int deg, inext, ilast;
      |                   ^~~~~
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:33:
In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4:
/data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable]
   14 |   double val;
      |          ^~~
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable]
  249 |     float a = std::stod(s);
      |           ^
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:5:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/formula.hpp:6:
/data/gannet/ripley/R/test-clang/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;
      |                   ^
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modelbits.hpp:6:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable]
  381 |   double au, av, qf;
      |              ^~
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:354:12: warning: unused variable 'result' [-Wunused-variable]
  354 |     double result = newuoa_closure( &closure, dim, control.npt, current_values.data(), control.rhobeg, control.rhoend, control.maxfun, w.data(), &fn_counter);
      |            ^~~~~~
/data/gannet/ripley/R/test-clang/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 gd_search.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
../inst/include/optim/optimderivatives.h:20:9: warning: unused variable 'curr_size' [-Wunused-variable]
   20 |     int curr_size = FirstOrderDerivatives.size();
      |         ^~~~~~~~~
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:10:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:26:
In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:46:
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Covariance' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Covariance>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:15:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/bobyqa_algo.h:201:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/bobyqa_general.h:251:1: warning: unused function 'bobyqa' [-Wunused-function]
  251 | bobyqa(const INTEGER n, const INTEGER npt,
      | ^~~~~~
In file included from gd_search.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field]
  413 |   int              iter = 0;
      |                    ^
25 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/glmmrBase/include' -I'/data/gannet/ripley/R/test-clang/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/rminqa/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -fopenmp  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c openmp_utils.cpp -o openmp_utils.o
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:19:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined]
   19 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
      |         ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here
   33 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
      |         ^
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:33:
In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3:
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable]
  145 |   int x ;
      |       ^
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable]
  415 |   double val;
      |          ^~~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable]
  625 |   double mem = 0;
      |          ^~~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable]
  626 |   int nz = Ap.back();
      |       ^~
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable]
  787 |   int ncmpa = 0 ;
      |       ^
/data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable]
  815 |   int deg, inext, ilast;
      |                   ^~~~~
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:33:
In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4:
/data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable]
   14 |   double val;
      |          ^~~
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:3:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable]
  249 |     float a = std::stod(s);
      |           ^
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:5:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/formula.hpp:6:
/data/gannet/ripley/R/test-clang/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;
      |                   ^
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modelbits.hpp:6:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable]
  381 |   double au, av, qf;
      |              ^~
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:354:12: warning: unused variable 'result' [-Wunused-variable]
  354 |     double result = newuoa_closure( &closure, dim, control.npt, current_values.data(), control.rhobeg, control.rhoend, control.maxfun, w.data(), &fn_counter);
      |            ^~~~~~
/data/gannet/ripley/R/test-clang/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 openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
../inst/include/optim/optimderivatives.h:20:9: warning: unused variable 'curr_size' [-Wunused-variable]
   20 |     int curr_size = FirstOrderDerivatives.size();
      |         ^~~~~~~~~
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:26:
In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:46:
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   31 |     delete obj;
      |     ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:15:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/bobyqa_algo.h:201:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/bobyqa_general.h:251:1: warning: unused function 'bobyqa' [-Wunused-function]
  251 | bobyqa(const INTEGER n, const INTEGER npt,
      | ^~~~~~
In file included from openmp_utils.cpp:2:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
In file included from ../inst/include/optim/optimderivatives.h:4:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr.h:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/model.hpp:8:
In file included from /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/modeloptim.hpp:12:
/data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field]
  413 |   int              iter = 0;
      |                    ^
24 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o glmmrOptim.so RcppExports.o gd_search.o openmp_utils.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/glmmrOptim/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/glmmrOptim/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/glmmrOptim/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)