* installing *source* package ‘glmmrOptim’ ...
** this is package ‘glmmrOptim’ version ‘0.3.7’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
using C++17
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppProgress/include' -I'/srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include' -I'/srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/BH/include' -I'/srv/hornik/tmp/CRAN_pretest/Library/rminqa/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3    -fpic  -g -O3 -Wall -pedantic   -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 /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 
      |         ^
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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:7:
In file included from ./../inst/include/optim/optimdata.h:4:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/matrixfield.h:4:
/srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:21:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined]
   21 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
      |         ^
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/covariance.hpp:7:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/formula.hpp:6:
/srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/formulaparse.h:12:11: warning: unused variable 'a' [-Wunused-variable]
   12 |     float a = std::stod(s);
      |           ^
/srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/formulaparse.h:235:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable]
  235 |   bool add_check, variable_in_data;
      |                   ^
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:22:9: warning: unused variable 'curr_size' [-Wunused-variable]
   22 |     int curr_size = FirstOrderDerivatives.size();
      |         ^~~~~~~~~
9 warnings generated.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppProgress/include' -I'/srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include' -I'/srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/BH/include' -I'/srv/hornik/tmp/CRAN_pretest/Library/rminqa/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3    -fpic  -g -O3 -Wall -pedantic   -c gd_search.cpp -o gd_search.o
In file included from gd_search.cpp:1:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/covariance.hpp:5:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:6:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/covariance.hpp:5:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:6:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 
      |         ^
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/covariance.hpp:5:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:6:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/covariance.hpp:5:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:6:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/covariance.hpp:5:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:6:
/srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:21:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined]
   21 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
      |         ^
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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 /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/covariance.hpp:7:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/formula.hpp:6:
/srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/formulaparse.h:12:11: warning: unused variable 'a' [-Wunused-variable]
   12 |     float a = std::stod(s);
      |           ^
/srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/formulaparse.h:235:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable]
  235 |   bool add_check, variable_in_data;
      |                   ^
In file included from gd_search.cpp:3:
In file included from ../inst/include/glmmrOptim.h:6:
In file included from ../inst/include/optim/optimclass.h:8:
../inst/include/optim/optimderivatives.h:22:9: warning: unused variable 'curr_size' [-Wunused-variable]
   22 |     int curr_size = FirstOrderDerivatives.size();
      |         ^~~~~~~~~
gd_search.cpp:24:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
   24 |      int a, b; // needed for defines on machines without openmp
      |          ^
In file included from gd_search.cpp:1:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/covariance.hpp:5:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:6:
In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:26:
In file included from /home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include/Rcpp.h:47:
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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;
      |     ^
/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/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>,
      |                          ^
11 warnings generated.
clang++-21 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-21/lib -Wl,-O1 -o glmmrOptim.so RcppExports.o gd_search.o -llapack -L/home/hornik/tmp/R-d-clang-21/lib -lRblas -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R-d-clang-21/lib -lR
installing to /srv/hornik/tmp/CRAN_pretest/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)