* 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: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c covariance_module.cpp -o covariance_module.o In file included from RcppExports.cpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from RcppExports.cpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c linpred_module.cpp -o linpred_module.o In file included from RcppExports.cpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ In file included from RcppExports.cpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c model_module.cpp -o model_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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c model_module_2.cpp -o model_module_2.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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c model_module_extension.cpp -o model_module_extension.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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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] #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here #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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:3: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] int x ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] double mem = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] int nz = Ap.back(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] int ncmpa = 0 ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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] #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here #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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:3: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] int x ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] double mem = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] int nz = Ap.back(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] int ncmpa = 0 ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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] #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here #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: ../inst/include/glmmr/general.h:249:11: warning: unused variable 'a' [-Wunused-variable] float a = std::stod(s); ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:3: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] int x ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] double mem = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] int nz = Ap.back(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] int ncmpa = 0 ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 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:19:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined] #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here #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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:3: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] int x ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.hIn 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] bool add_check, variable_in_data; ^ :415:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] double mem = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] int nz = Ap.back(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] int ncmpa = 0 ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 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] float a = std::stod(s); ^ 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] #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here #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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:3: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] int x ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] double mem = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] int nz = Ap.back(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] int ncmpa = 0 ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ 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] bool add_check, variable_in_data; ^ 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] float a = std::stod(s); ^ 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] double au, av, qf; ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c openmp_utils.cpp -o openmp_utils.o 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] 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] 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: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] 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] double a = eval(current_values, g); ^ 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] double au, av, qf; ^ 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] bool add_check, variable_in_data; ^ 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] float a = std::stod(s); ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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: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] 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] double a = eval(current_values, g); ^ 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] double au, av, qf; ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 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] 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] 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] 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] double a = eval(current_values, g); ^ 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] 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] 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] double a = eval(current_values, g); ^ 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] #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here #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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:3: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] int x ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] double mem = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] int nz = Ap.back(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] int ncmpa = 0 ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ 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] 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] double a = eval(current_values, g); ^ 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] 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] 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] 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] 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] double a = eval(current_values, g); ^ openmp_utils.cpp:18:9: warning: variable 'a' set but not used [-Wunused-but-set-variable] int a, b; // needed for defines on machines without openmp ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp.h:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp.h:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp.h:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp.h:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp.h:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer' requested here 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] 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] int iter = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer' requested here 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] 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] int iter = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>' requested here 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] 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] int iter = 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp.h:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here 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] int iter = 0; ^ 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] 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] int iter = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here 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] 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] int iter = 0; ^ 24 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 24 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_mcml_bernoulli.cc -o stanExports_mcml_bernoulli.o 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] #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here #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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:3: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable] int x ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:415:10: warning: unused variable 'val' [-Wunused-variable] double val; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:625:10: warning: unused variable 'mem' [-Wunused-variable] double mem = 0; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:626:7: warning: unused variable 'nz' [-Wunused-variable] int nz = Ap.back(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:787:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable] int ncmpa = 0 ; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/sparsematrix.h:815:19: warning: unused variable 'ilast' [-Wunused-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/SparseChol.h:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable] 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] 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] bool add_check, variable_in_data; ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ 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] double au, av, qf; ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 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] 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] double a = eval(current_values, g); ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] struct ops_partials_edge> { ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct 26 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_mcml_beta.cc -o stanExports_mcml_beta.o In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 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] constexpr bool jacobian__ = false; ^ ./stanExports_mcml_bernoulli.h:306:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ ./stanExports_mcml_bernoulli.h:332:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp.h:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ In file included from stanExports_mcml_bernoulli.cc:5: In file included from ./stanExports_mcml_bernoulli.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/beta.hpp:1721: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 rx = detail::ibeta_inv_imp( ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return ibeta_inv(a, b, p, static_cast(nullptr), pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] struct ops_partials_edge> { ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here void Finalizer(T*) = standard_delete_finalizer, ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] delete obj; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer>>' requested here 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] 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] int iter = 0; ^ In file included from stanExports_mcml_beta.cc:5: In file included from ./stanExports_mcml_beta.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 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] constexpr bool jacobian__ = false; ^ ./stanExports_mcml_beta.h:313:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ ./stanExports_mcml_beta.h:339:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/beta.hpp:1721: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 rx = detail::ibeta_inv_imp( ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return ibeta_inv(a, b, p, static_cast(nullptr), pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 23 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] struct ops_partials_edge> { ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 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] constexpr bool jacobian__ = false; ^ ./stanExports_mcml_binomial.h:319:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ ./stanExports_mcml_binomial.h:345:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/beta.hpp:1721: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 rx = detail::ibeta_inv_imp( ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return ibeta_inv(a, b, p, static_cast(nullptr), pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 25 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ 13 warnings generated. In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_mcml_gaussian.cc -o stanExports_mcml_gaussian.o In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 24 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I/opt/R/x86_64/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_mcml_poisson.cc -o stanExports_mcml_poisson.o In file included from stanExports_mcml_gamma.cc:5: In file included from ./stanExports_mcml_gamma.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] struct ops_partials_edge> { ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ 22 warnings generated. In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] struct ops_partials_edge> { ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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] struct ops_partials_edge> { ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 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] constexpr bool jacobian__ = false; ^ ./stanExports_mcml_gamma.h:313:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ ./stanExports_mcml_gamma.h:339:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/beta.hpp:1721: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 rx = detail::ibeta_inv_imp( ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return ibeta_inv(a, b, p, static_cast(nullptr), pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 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] constexpr bool jacobian__ = false; ^ ./stanExports_mcml_gaussian.h:302:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ ./stanExports_mcml_gaussian.h:328:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 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] constexpr bool jacobian__ = false; ^ ./stanExports_mcml_poisson.h:272:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ ./stanExports_mcml_poisson.h:298:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ 13 warnings generated. In file included from stanExports_mcml_gaussian.cc:5: In file included from ./stanExports_mcml_gaussian.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/beta.hpp:1721: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 rx = detail::ibeta_inv_imp( ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return ibeta_inv(a, b, p, static_cast(nullptr), pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ In file included from stanExports_mcml_poisson.cc:5: In file included from ./stanExports_mcml_poisson.h:23: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/beta.hpp:1721: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 rx = detail::ibeta_inv_imp( ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return ibeta_inv(a, b, p, static_cast(nullptr), pol); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 13 warnings generated. 13 warnings generated. 13 warnings generated. 13 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -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/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/lib/ -Wl,-rpath,/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/lib/ -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/glmmrBase.Rcheck/00LOCK-glmmrBase/00new/glmmrBase/libs ** generating debug symbols (dSYM) ** 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)