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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IgGeneUsage
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘IgGeneUsage’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_dgu.cc -o stanExports_dgu.o
In file included from stanExports_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu.cc:5:
./stanExports_dgu.h:925:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
int pos__ = std::numeric_limits<int>::min();
^
In file included from stanExports_dgu.cc:5:
In file included from ./stanExports_dgu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
rx = detail::ibeta_inv_imp(
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
^
11 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_dgu_paired.cc -o stanExports_dgu_paired.o
In file included from stanExports_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired.cc:5:
./stanExports_dgu_paired.h:975:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
int pos__ = std::numeric_limits<int>::min();
^
In file included from stanExports_dgu_paired.cc:5:
In file included from ./stanExports_dgu_paired.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
rx = detail::ibeta_inv_imp(
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
^
11 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_dgu_paired_rep.cc -o stanExports_dgu_paired_rep.o
In file included from stanExports_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_paired_rep.cc:5:
./stanExports_dgu_paired_rep.h:1062:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
int pos__ = std::numeric_limits<int>::min();
^
In file included from stanExports_dgu_paired_rep.cc:5:
In file included from ./stanExports_dgu_paired_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
rx = detail::ibeta_inv_imp(
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
^
11 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_dgu_rep.cc -o stanExports_dgu_rep.o
In file included from stanExports_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_dgu_rep.cc:5:
./stanExports_dgu_rep.h:1055:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
int pos__ = std::numeric_limits<int>::min();
^
In file included from stanExports_dgu_rep.cc:5:
In file included from ./stanExports_dgu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
rx = detail::ibeta_inv_imp(
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
^
11 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_gu.cc -o stanExports_gu.o
In file included from stanExports_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu.cc:5:
./stanExports_gu.h:670:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
int pos__ = std::numeric_limits<int>::min();
^
In file included from stanExports_gu.cc:5:
In file included from ./stanExports_gu.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
rx = detail::ibeta_inv_imp(
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
^
11 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_gu_rep.cc -o stanExports_gu_rep.o
In file included from stanExports_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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_gu_rep.cc:5:
./stanExports_gu_rep.h:802:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
int pos__ = std::numeric_limits<int>::min();
^
In file included from stanExports_gu_rep.cc:5:
In file included from ./stanExports_gu_rep.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
rx = detail::ibeta_inv_imp(
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
^
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 IgGeneUsage.so RcppExports.o stanExports_dgu.o stanExports_dgu_paired.o stanExports_dgu_paired_rep.o stanExports_dgu_rep.o stanExports_gu.o stanExports_gu_rep.o -L/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-IgGeneUsage/00new/IgGeneUsage/libs
** R
** data
** 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 (IgGeneUsage)