* installing *source* package ‘glmmrOptim’ ... ** package ‘glmmrOptim’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 19.1.5’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/glmmrOptim/src' /usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c gd_search.cpp -o gd_search.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -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 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 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 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 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 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 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 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 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 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:37: 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:437:10: warning: unused variable 'val' [-Wunused-variable] 437 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:647:10: warning: unused variable 'mem' [-Wunused-variable] 647 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:648:7: warning: unused variable 'nz' [-Wunused-variable] 648 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:809:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 809 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/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 /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:37: 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: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:37: 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:437:10: warning: unused variable 'val' [-Wunused-variable] 437 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:647:10: warning: unused variable 'mem' [-Wunused-variable] 647 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:648:7: warning: unused variable 'nz' [-Wunused-variable] 648 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:809:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 809 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:837:19: warning: unused variable 'ilast' [-Wunused-variable] 837 | 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:37: 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: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:37: 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:437:10: warning: unused variable 'val' [-Wunused-variable] 437 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:647:10: warning: unused variable 'mem' [-Wunused-variable] 647 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:648:7: warning: unused variable 'nz' [-Wunused-variable] 648 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:809:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 809 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/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 /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:37: 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:257:11: warning: unused variable 'a' [-Wunused-variable] 257 | 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:3: /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:257:11: warning: unused variable 'a' [-Wunused-variable] 257 | 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:3: /data/gannet/ripley/R/test-clang/glmmrBase/include/glmmr/general.h:257:11: warning: unused variable 'a' [-Wunused-variable] 257 | 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:207:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 207 | 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: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:207:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 207 | 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: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:207:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 207 | 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:379:14: warning: unused variable 'av' [-Wunused-variable] 379 | 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: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:379:14: warning: unused variable 'av' [-Wunused-variable] 379 | 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: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:379:14: warning: unused variable 'av' [-Wunused-variable] 379 | 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 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 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 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 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 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 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>, | ^ 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>, | ^ 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>, | ^ /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::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; | ^ 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; | ^ 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. 24 warnings generated. 25 warnings generated. /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/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 -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)