* installing *source* package ‘glmmrBase’ ... ** package ‘glmmrBase’ successfully unpacked and MD5 sums checked ** using staged installation Warning message: In .warning_nowrite(file.path(basename(pkgdir), ...)) : 'glmmrBase/src/Makevars' already exists. Not overwritten by rstantools.FALSE ** libs using C++ compiler: ‘clang version 18.1.4’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/glmmrBase/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /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. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c covariance_module.cpp -o covariance_module.o In file included from covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/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 covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3: /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] 415 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] 625 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] 626 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 787 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 815 | int deg, inext, ilast; | ^~~~~ In file included from covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4: /data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 14 | double val; | ^~~ In file included from covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable] 249 | float a = std::stod(s); | ^ In file included from covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:5: In file included from ../inst/include/glmmr/formula.hpp:6: ../inst/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 208 | bool add_check, variable_in_data; | ^ In file included from covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:4: In file included from ../inst/include/glmmr/modelbits.hpp:6: ../inst/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable] 381 | double au, av, qf; | ^~ In file included from covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/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); | ^~~~~~ ../inst/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable] 503 | double a = eval(current_values, g); | ^ In file included from covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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:46: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /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' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /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' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /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' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ In file included from covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: In file included from ../inst/include/glmmr/optim/optim.h:15: In file included from ../inst/include/glmmr/optim/bobyqa_algo.h:201: ../inst/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 covariance_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field] 413 | int iter = 0; | ^ 26 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c linpred_module.cpp -o linpred_module.o In file included from linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/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 linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3: /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] 415 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] 625 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] 626 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 787 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 815 | int deg, inext, ilast; | ^~~~~ In file included from linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4: /data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 14 | double val; | ^~~ In file included from linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable] 249 | float a = std::stod(s); | ^ In file included from linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:5: In file included from ../inst/include/glmmr/formula.hpp:6: ../inst/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 208 | bool add_check, variable_in_data; | ^ In file included from linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:4: In file included from ../inst/include/glmmr/modelbits.hpp:6: ../inst/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable] 381 | double au, av, qf; | ^~ In file included from linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/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); | ^~~~~~ ../inst/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable] 503 | double a = eval(current_values, g); | ^ In file included from linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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:46: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /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' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ In file included from linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: In file included from ../inst/include/glmmr/optim/optim.h:15: In file included from ../inst/include/glmmr/optim/bobyqa_algo.h:201: ../inst/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 linpred_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field] 413 | int iter = 0; | ^ 24 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c model_module.cpp -o model_module.o In file included from model_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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:3: 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:3: 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:3: 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:3: ../inst/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 model_module.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3: /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] 415 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] 625 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] 626 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 787 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 815 | int deg, inext, ilast; | ^~~~~ In file included from model_module.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4: /data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 14 | double val; | ^~~ In file included from model_module.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable] 249 | float a = std::stod(s); | ^ In file included from model_module.cpp:1: In file included from ../inst/include/glmmr.h:5: In file included from ../inst/include/glmmr/formula.hpp:6: ../inst/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 208 | bool add_check, variable_in_data; | ^ In file included from model_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:4: In file included from ../inst/include/glmmr/modelbits.hpp:6: ../inst/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable] 381 | double au, av, qf; | ^~ In file included from model_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/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); | ^~~~~~ ../inst/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable] 503 | double a = eval(current_values, g); | ^ In file included from model_module.cpp:1: In file included from ../inst/include/glmmr.h:3: 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:46: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::ModelBits' 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>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ In file included from model_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: In file included from ../inst/include/glmmr/optim/optim.h:15: In file included from ../inst/include/glmmr/optim/bobyqa_algo.h:201: ../inst/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 model_module.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field] 413 | int iter = 0; | ^ 24 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c model_module_2.cpp -o model_module_2.o In file included from model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:3: 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_2.cpp:1: In file included from ../inst/include/glmmr.h:3: 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_2.cpp:1: In file included from ../inst/include/glmmr.h:3: 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_2.cpp:1: In file included from ../inst/include/glmmr.h:3: 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_2.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/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 model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3: /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] 415 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] 625 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] 626 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 787 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 815 | int deg, inext, ilast; | ^~~~~ In file included from model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4: /data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 14 | double val; | ^~~ In file included from model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable] 249 | float a = std::stod(s); | ^ In file included from model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:5: In file included from ../inst/include/glmmr/formula.hpp:6: ../inst/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 208 | bool add_check, variable_in_data; | ^ In file included from model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:4: In file included from ../inst/include/glmmr/modelbits.hpp:6: ../inst/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable] 381 | double au, av, qf; | ^~ In file included from model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/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); | ^~~~~~ ../inst/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable] 503 | double a = eval(current_values, g); | ^ In file included from model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:3: 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:46: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ In file included from model_module_2.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field] 413 | int iter = 0; | ^ 22 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c model_module_extension.cpp -o model_module_extension.o In file included from model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: 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_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: 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_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: 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_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: 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_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/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 model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3: /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] 415 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] 625 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] 626 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 787 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 815 | int deg, inext, ilast; | ^~~~~ In file included from model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4: /data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 14 | double val; | ^~~ In file included from model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable] 249 | float a = std::stod(s); | ^ In file included from model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:5: In file included from ../inst/include/glmmr/formula.hpp:6: ../inst/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 208 | bool add_check, variable_in_data; | ^ In file included from model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:4: In file included from ../inst/include/glmmr/modelbits.hpp:6: ../inst/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable] 381 | double au, av, qf; | ^~ In file included from model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/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); | ^~~~~~ ../inst/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable] 503 | double a = eval(current_values, g); | ^ In file included from model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:3: 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:46: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /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' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /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' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ In file included from model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: In file included from ../inst/include/glmmr/optim/optim.h:15: In file included from ../inst/include/glmmr/optim/bobyqa_algo.h:201: ../inst/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 model_module_extension.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field] 413 | int iter = 0; | ^ 25 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c openmp_utils.cpp -o openmp_utils.o In file included from openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/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:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3: /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] 415 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] 625 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] 626 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 787 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 815 | int deg, inext, ilast; | ^~~~~ In file included from openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4: /data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 14 | double val; | ^~~ In file included from openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable] 249 | float a = std::stod(s); | ^ In file included from openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:5: In file included from ../inst/include/glmmr/formula.hpp:6: ../inst/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 208 | bool add_check, variable_in_data; | ^ In file included from openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:4: In file included from ../inst/include/glmmr/modelbits.hpp:6: ../inst/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable] 381 | double au, av, qf; | ^~ In file included from openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/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); | ^~~~~~ ../inst/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable] 503 | double a = eval(current_values, g); | ^ openmp_utils.cpp:18:9: warning: variable 'a' set but not used [-Wunused-but-set-variable] 18 | int a, b; // needed for defines on machines without openmp | ^ In file included from openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:3: 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:46: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ In file included from openmp_utils.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: In file included from ../inst/include/glmmr/optim/optim.h:15: In file included from ../inst/include/glmmr/optim/bobyqa_algo.h:201: ../inst/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:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field] 413 | int iter = 0; | ^ 24 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c other_functions.cpp -o other_functions.o In file included from other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: 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 other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/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 other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:3: /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] 145 | int x ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] 415 | double val; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] 625 | double mem = 0; | ^~~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] 626 | int nz = Ap.back(); | ^~ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] 787 | int ncmpa = 0 ; | ^ /data/gannet/ripley/R/test-clang/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 815 | int deg, inext, ilast; | ^~~~~ In file included from other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: In file included from ../inst/include/glmmr/general.h:33: In file included from /data/gannet/ripley/R/test-clang/SparseChol/include/SparseChol.h:4: /data/gannet/ripley/R/test-clang/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 14 | double val; | ^~~ In file included from other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: ../inst/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable] 249 | float a = std::stod(s); | ^ In file included from other_functions.cpp:1: In file included from ../inst/include/glmmr.h:5: In file included from ../inst/include/glmmr/formula.hpp:6: ../inst/include/glmmr/formulaparse.h:208:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable] 208 | bool add_check, variable_in_data; | ^ In file included from other_functions.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:4: In file included from ../inst/include/glmmr/modelbits.hpp:6: ../inst/include/glmmr/nngpcovariance.hpp:381:14: warning: unused variable 'av' [-Wunused-variable] 381 | double au, av, qf; | ^~ In file included from other_functions.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/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); | ^~~~~~ ../inst/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable] 503 | double a = eval(current_values, g); | ^ In file included from other_functions.cpp:1: In file included from ../inst/include/glmmr.h:3: 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:46: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model>' 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>>' requested here 54 | void Finalizer(T*) = standard_delete_finalizer, | ^ In file included from other_functions.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: In file included from ../inst/include/glmmr/optim/optim.h:15: In file included from ../inst/include/glmmr/optim/bobyqa_algo.h:201: ../inst/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 other_functions.cpp:1: In file included from ../inst/include/glmmr.h:8: In file included from ../inst/include/glmmr/model.hpp:8: In file included from ../inst/include/glmmr/modeloptim.hpp:12: ../inst/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field] 413 | int iter = 0; | ^ 23 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stanExports_mcml_bernoulli.cc -o stanExports_mcml_bernoulli.o In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^ In file included from stanExports_mcml_bernoulli.cc:5: ./stanExports_mcml_bernoulli.h:269:20: warning: unused variable 'jacobian__' [-Wunused-variable] 269 | constexpr bool jacobian__ = false; | ^~~~~~~~~~ ./stanExports_mcml_bernoulli.h:306:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 306 | int pos__ = std::numeric_limits::min(); | ^ ./stanExports_mcml_bernoulli.h:332:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 332 | int pos__ = std::numeric_limits::min(); | ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 21 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stanExports_mcml_beta.cc -o stanExports_mcml_beta.o In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^ In file included from stanExports_mcml_beta.cc:5: ./stanExports_mcml_beta.h:262:20: warning: unused variable 'jacobian__' [-Wunused-variable] 262 | constexpr bool jacobian__ = false; | ^~~~~~~~~~ ./stanExports_mcml_beta.h:313:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 313 | int pos__ = std::numeric_limits::min(); | ^ ./stanExports_mcml_beta.h:339:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 339 | int pos__ = std::numeric_limits::min(); | ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 21 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stanExports_mcml_binomial.cc -o stanExports_mcml_binomial.o In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^ In file included from stanExports_mcml_binomial.cc:5: ./stanExports_mcml_binomial.h:282:20: warning: unused variable 'jacobian__' [-Wunused-variable] 282 | constexpr bool jacobian__ = false; | ^~~~~~~~~~ ./stanExports_mcml_binomial.h:319:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 319 | int pos__ = std::numeric_limits::min(); | ^ ./stanExports_mcml_binomial.h:345:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 345 | int pos__ = std::numeric_limits::min(); | ^ In file included from stanExports_mcml_binomial.cc:5: In file included from ./stanExports_mcml_binomial.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 21 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stanExports_mcml_gamma.cc -o stanExports_mcml_gamma.o In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^ In file included from stanExports_mcml_gamma.cc:5: ./stanExports_mcml_gamma.h:276:20: warning: unused variable 'jacobian__' [-Wunused-variable] 276 | constexpr bool jacobian__ = false; | ^~~~~~~~~~ ./stanExports_mcml_gamma.h:313:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 313 | int pos__ = std::numeric_limits::min(); | ^ ./stanExports_mcml_gamma.h:339:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 339 | int pos__ = std::numeric_limits::min(); | ^ In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 21 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stanExports_mcml_gaussian.cc -o stanExports_mcml_gaussian.o In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^ In file included from stanExports_mcml_gaussian.cc:5: ./stanExports_mcml_gaussian.h:265:20: warning: unused variable 'jacobian__' [-Wunused-variable] 265 | constexpr bool jacobian__ = false; | ^~~~~~~~~~ ./stanExports_mcml_gaussian.h:302:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 302 | int pos__ = std::numeric_limits::min(); | ^ ./stanExports_mcml_gaussian.h:328:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 328 | int pos__ = std::numeric_limits::min(); | ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 21 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -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/SparseChol/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stanExports_mcml_poisson.cc -o stanExports_mcml_poisson.o In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: 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 stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: 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 stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^ In file included from stanExports_mcml_poisson.cc:5: ./stanExports_mcml_poisson.h:235:20: warning: unused variable 'jacobian__' [-Wunused-variable] 235 | constexpr bool jacobian__ = false; | ^~~~~~~~~~ ./stanExports_mcml_poisson.h:272:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 272 | int pos__ = std::numeric_limits::min(); | ^ ./stanExports_mcml_poisson.h:298:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 298 | int pos__ = std::numeric_limits::min(); | ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::overflow_error, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 21 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o glmmrBase.so RcppExports.o covariance_module.o linpred_module.o model_module.o model_module_2.o model_module_extension.o openmp_utils.o other_functions.o stanExports_mcml_bernoulli.o stanExports_mcml_beta.o stanExports_mcml_binomial.o stanExports_mcml_gamma.o stanExports_mcml_gaussian.o stanExports_mcml_poisson.o -L/data/gannet/ripley/R/test-clang/RcppParallel/lib/ -Wl,-rpath,/data/gannet/ripley/R/test-clang/RcppParallel/lib/ -ltbb -ltbbmalloc -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/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)