* installing *source* package ‘EpiPvr’ ... ** this is package ‘EpiPvr’ version ‘0.0.1’ ** package ‘EpiPvr’ successfully unpacked and MD5 sums checked ** using staged installation Warning message: In .warning_nowrite(file.path(basename(pkgdir), ...)) : 'EpiPvr/src/Makevars' already exists. Not overwritten by rstantools.FALSE ** libs using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’ using C++17 using SDK: ‘MacOSX14.5.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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/sonoma-arm64/Rlib/4.6/BH/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include' -I/opt/R/arm64/include -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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/sonoma-arm64/Rlib/4.6/BH/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include' -I/opt/R/arm64/include -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_APmodel_PT_virus.cc -o stanExports_APmodel_PT_virus.o In file included from RcppExports.cpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from RcppExports.cpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from RcppExports.cpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from RcppExports.cpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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/sonoma-arm64/Rlib/4.6/BH/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include' -I/opt/R/arm64/include -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_APmodel_SPT_virus.cc -o stanExports_APmodel_SPT_virus.o 5 warnings generated. In file included from stanExports_APmodel_PT_virus.cc:5: In file included from ./stanExports_APmodel_PT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stanExports_APmodel_PT_virus.cc:5: In file included from ./stanExports_APmodel_PT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stanExports_APmodel_PT_virus.cc:5: In file included from ./stanExports_APmodel_PT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/streambuf:295:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 295 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_APmodel_PT_virus.cc:5: In file included from ./stanExports_APmodel_PT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/streambuf:295:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 295 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_APmodel_PT_virus.cc:5: In file included from ./stanExports_APmodel_PT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stanExports_APmodel_PT_virus.cc:5: In file included from ./stanExports_APmodel_PT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stanExports_APmodel_SPT_virus.cc:5: In file included from ./stanExports_APmodel_SPT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stanExports_APmodel_SPT_virus.cc:5: In file included from ./stanExports_APmodel_SPT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:3: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stanExports_APmodel_PT_virus.cc:5: In file included from ./stanExports_APmodel_PT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stanExports_APmodel_SPT_virus.cc:5: In file included from ./stanExports_APmodel_SPT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/streambuf:295:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 295 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_APmodel_SPT_virus.cc:5: In file included from ./stanExports_APmodel_SPT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:21: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/streambuf:295:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 295 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stanExports_APmodel_SPT_virus.cc:5: In file included from ./stanExports_APmodel_SPT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stanExports_APmodel_SPT_virus.cc:5: In file included from ./stanExports_APmodel_SPT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:31: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stanExports_APmodel_SPT_virus.cc:5: In file included from ./stanExports_APmodel_SPT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:43: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stanExports_APmodel_PT_virus.cc:5: In file included from ./stanExports_APmodel_PT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^ In file included from stanExports_APmodel_PT_virus.cc:5: ./stanExports_APmodel_PT_virus.h:1855:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 1855 | int pos__ = std::numeric_limits::min(); | ^ ./stanExports_APmodel_PT_virus.h:1920:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 1920 | int pos__ = std::numeric_limits::min(); | ^ In file included from stanExports_APmodel_SPT_virus.cc:5: In file included from ./stanExports_APmodel_SPT_virus.h:23: In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4: /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^ In file included from stanExports_APmodel_SPT_virus.cc:5: ./stanExports_APmodel_SPT_virus.h:1248:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 1248 | int pos__ = std::numeric_limits::min(); | ^ ./stanExports_APmodel_SPT_virus.h:1303:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 1303 | int pos__ = std::numeric_limits::min(); | ^ 11 warnings generated. 11 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o EpiPvr.so RcppExports.o stanExports_APmodel_PT_virus.o stanExports_APmodel_SPT_virus.o -L/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/lib -ltbb -ltbbmalloc -L/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/lib/ -Wl,-rpath,/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R ld: warning: ignoring duplicate libraries: '-ltbb', '-ltbbmalloc' installing to /Volumes/Builds/packages/sonoma-arm64/results/4.6/EpiPvr.Rcheck/00LOCK-EpiPvr/00new/EpiPvr/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 ** installing vignettes ** 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 (EpiPvr)