* installing *source* package ‘glmmrBase’ ...
** this is package ‘glmmrBase’ version ‘1.4.0’
** package ‘glmmrBase’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘clang version 22.1.5 (https://github.com/llvm/llvm-project 5ea218a153f4d2f815b8244eab3e4b4ba5e00e6c)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/glmmrBase/src'
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -D_HAS_AUTO_PTR_ETC=0  -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/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp: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 /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 /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 /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;
      |       ^
5 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -D_HAS_AUTO_PTR_ETC=0  -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/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c model_module.cpp -o model_module.o
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:4:
In file included from ../inst/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 model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:4:
In file included from ../inst/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 model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:4:
In file included from ../inst/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 model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:4:
In file included from ../inst/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 model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:4:
../inst/include/glmmr/general.h:21:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined]
   21 | #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 model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:5:
In file included from ../inst/include/glmmr/modelbits.hpp:3:
In file included from ../inst/include/glmmr/covariance.hpp:7:
In file included from ../inst/include/glmmr/formula.hpp:6:
../inst/include/glmmr/formulaparse.h:12:11: warning: unused variable 'a' [-Wunused-variable]
   12 |     float a = std::stod(s);
      |           ^
../inst/include/glmmr/formulaparse.h:235:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable]
  235 |   bool add_check, variable_in_data;
      |                   ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:5:
In file included from ../inst/include/glmmr/modelbits.hpp:4:
../inst/include/glmmr/hsgpcovariance.hpp:203:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
  203 |     shift_.resize(dim);
      |     ^
../inst/include/glmmr/hsgpcovariance.hpp:192:3: note: previous statement is here
  192 |   for (int k=0; k<matD.outerSize(); ++k)
      |   ^
../inst/include/glmmr/hsgpcovariance.hpp:330:14: warning: unused variable 'old_scale' [-Wunused-variable]
  330 |       double old_scale = scale_factors_.maxCoeff(); // previous isotropic scale
      |              ^~~~~~~~~
../inst/include/glmmr/hsgpcovariance.hpp:347:12: warning: unused variable 'old_scale_0' [-Wunused-variable]
  347 |     double old_scale_0 = scale_factors_(0); // any dim, since about to go isotropic
      |            ^~~~~~~~~~~
../inst/include/glmmr/hsgpcovariance.hpp:422:10: warning: unused variable 'sigma2' [-Wunused-variable]
  422 |   double sigma2 = logpars ? exp(parameters_[0]) : parameters_[0];
      |          ^~~~~~
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:7:
../inst/include/glmmr/modelmatrix.hpp:161:13: warning: unused variable 'P_' [-Wunused-variable]
  161 |   const int P_ = P();
      |             ^~
../inst/include/glmmr/modelmatrix.hpp:162:13: warning: unused variable 'M' [-Wunused-variable]
  162 |   const int M = model.covariance.Q();
      |             ^
../inst/include/glmmr/modelmatrix.hpp:206:13: warning: unused variable 'P_' [-Wunused-variable]
  206 |   const int P_ = P();
      |             ^~
../inst/include/glmmr/modelmatrix.hpp:775:15: warning: unused variable 'Mdim' [-Wunused-variable]
  775 |     const int Mdim = Z.cols();
      |               ^~~~
../inst/include/glmmr/modelmatrix.hpp:727:13: warning: unused variable 'Pdim' [-Wunused-variable]
  727 |   const int Pdim = P();
      |             ^~~~
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:8:
In file included from ../inst/include/glmmr/modeloptim.hpp:8:
../inst/include/glmmr/optim/optim.h:353:12: warning: unused variable 'result' [-Wunused-variable]
  353 |     double result = newuoa_closure( &closure, dim, control.npt, current_values.data(), control.rhobeg, control.rhoend, control.maxfun, w.data(), &fn_counter);
      |            ^~~~~~
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:8:
../inst/include/glmmr/modeloptim.hpp:244:7: warning: unused variable 'p' [-Wunused-variable]
  244 |   int p = model.linear_predictor.P();
      |       ^
../inst/include/glmmr/modeloptim.hpp:245:7: warning: unused variable 'Mspec' [-Wunused-variable]
  245 |   int Mspec = model.covariance.Q();
      |       ^~~~~
../inst/include/glmmr/modeloptim.hpp:901:7: warning: unused variable 'n' [-Wunused-variable]
  901 |   int n = model.data.y.size();
      |       ^
../inst/include/glmmr/modeloptim.hpp:902:7: warning: unused variable 'Mspec' [-Wunused-variable]
  902 |   int Mspec = model.covariance.Q();
      |       ^~~~~
../inst/include/glmmr/modeloptim.hpp:1148:7: warning: unused variable 'n' [-Wunused-variable]
 1148 |   int n = model.data.y.size();
      |       ^
model_module.cpp:2464:8: warning: variable 'a' set but not used [-Wunused-but-set-variable]
 2464 |    int a, b; // needed for defines on machines without openmp
      |        ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/model.hpp:4:
In file included from ../inst/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:47:
/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::Model<glmmr::ModelBits<glmmr::ar1Covariance, 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::ar1Covariance, 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::spdeCovariance, 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::spdeCovariance, 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::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::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>,
      |                          ^
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::nngpCovariance' 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::nngpCovariance>' 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::hsgpCovariance' 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::hsgpCovariance>' 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::ar1Covariance' 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::ar1Covariance>' 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::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::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>' requested here
   54 |     void Finalizer(T*) = standard_delete_finalizer<T>,
      |                          ^
35 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o glmmrBase.so RcppExports.o model_module.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/glmmrBase/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/glmmrBase/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/glmmrBase/src'
installing to /data/gannet/ripley/R/packages/tests-clang/glmmrBase.Rcheck/00LOCK-glmmrBase/00new/glmmrBase/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (glmmrBase)