* installing *source* package ‘glmmrOptim’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 19.1.5 (1)’ using C++17 clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/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/4.5/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 -DR_NO_REMAP -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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.5/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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.5/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/4.5/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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.5/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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.5/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: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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: /srv/hornik/tmp/CRAN_pretest/Library/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 | ^ /home/hornik/lib/R/Library/4.5/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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:34: In file included from /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/SparseChol.h:3: /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:437:10: warning: unused variable 'val' [-Wunused-variable] 437 | double val; | ^~~ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:647:10: warning: unused variable 'mem' [-Wunused-variable] 647 | double mem = 0; | ^~~ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:648:7: warning: unused variable 'nz' [-Wunused-variable] 648 | int nz = Ap.back(); | ^~ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:809:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 809 | int ncmpa = 0 ; | ^ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:837:19: warning: unused variable 'ilast' [-Wunused-variable] 837 | 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 /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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:34: In file included from /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/SparseChol.h:4: /srv/hornik/tmp/CRAN_pretest/Library/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 /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: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 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(); | ^~~~~~~~~ 16 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/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/4.5/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 -DR_NO_REMAP -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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: 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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.5/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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: 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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.5/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/4.5/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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: 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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.5/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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: 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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.5/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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: /srv/hornik/tmp/CRAN_pretest/Library/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 | ^ /home/hornik/lib/R/Library/4.5/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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/maths.h:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:34: In file included from /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/SparseChol.h:3: /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:437:10: warning: unused variable 'val' [-Wunused-variable] 437 | double val; | ^~~ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:647:10: warning: unused variable 'mem' [-Wunused-variable] 647 | double mem = 0; | ^~~ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:648:7: warning: unused variable 'nz' [-Wunused-variable] 648 | int nz = Ap.back(); | ^~ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:809:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 809 | int ncmpa = 0 ; | ^ /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/sparsematrix.h:837:19: warning: unused variable 'ilast' [-Wunused-variable] 837 | int deg, inext, ilast; | ^~~~~ 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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/general.h:34: In file included from /srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include/SparseChol.h:4: /srv/hornik/tmp/CRAN_pretest/Library/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 /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: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 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:23:10: warning: variable 'a' set but not used [-Wunused-but-set-variable] 23 | 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:5: In file included from /srv/hornik/tmp/CRAN_pretest/Library/glmmrBase/include/glmmr/algo.h:3: 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/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:26: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include/Rcpp.h:46: /home/hornik/lib/R/Library/4.5/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/4.5/x86_64-linux-gnu/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ 18 warnings generated. clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-19/lib -Wl,-O1 -o glmmrOptim.so RcppExports.o gd_search.o -llapack -L/home/hornik/tmp/R-d-clang-19/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R-d-clang-19/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)