##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ppcseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ppcseq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_negBinomial_MPI.cc -o stanExports_negBinomial_MPI.o
In file included from stanExports_negBinomial_MPI.cc:5:
In file included from ./stanExports_negBinomial_MPI.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 ('std::streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_negBinomial_MPI.cc:5:
In file included from ./stanExports_negBinomial_MPI.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 ('std::streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_negBinomial_MPI.cc:5:
In file included from ./stanExports_negBinomial_MPI.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/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_negBinomial_MPI.cc:5:
In file included from ./stanExports_negBinomial_MPI.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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_negBinomial_MPI.cc:5:
./stanExports_negBinomial_MPI.h:1422:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
In file included from stanExports_negBinomial_MPI.cc:5:
In file included from ./stanExports_negBinomial_MPI.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here
   return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
          ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here
  return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
                      ^
In file included from stanExports_negBinomial_MPI.cc:5:
./stanExports_negBinomial_MPI.h:438:15: warning: unused variable 'global_parameters' [-Wunused-variable]
  const auto& global_parameters = stan::math::to_ref(global_parameters_arg__);
              ^
./stanExports_negBinomial_MPI.h:242:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce<Eigen::Matrix<double, -1, 1, 0>, Eigen::Matrix<double, -1, 1, 0>, double, nullptr>' requested here
    return lp_reduce(global_parameters, local_parameters, real_data,
           ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect_reduce.hpp:47:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()<Eigen::Matrix<double, -1, 1, 0>, Eigen::Matrix<double, -1, 1, 0>, double, nullptr>' requested here
    return F()(shared_params, job_specific_params, x_r, x_i, msgs).transpose();
           ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:23: note: in instantiation of member function 'stan::math::internal::map_rect_reduce<model_negBinomial_MPI_namespace::lp_reduce_functor__, double, double>::operator()' requested here
      job_output[i] = ReduceF()(shared_params_dbl, value_of(job_params[i]),
                      ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:183:20: note: in instantiation of function template specialization 'stan::math::internal::map_rect_concurrent<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, const Eigen::Map<Eigen::Matrix<double, -1, 1, 0>, 0> &, double, nullptr>' requested here
  return internal::map_rect_concurrent<call_id, F, T_shared_param_ref,
                   ^
./stanExports_negBinomial_MPI.h:1246:38: note: in instantiation of function template specialization 'stan::math::map_rect<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, Eigen::Map<Eigen::Matrix<double, -1, 1, 0>, 0>, double, nullptr>' requested here
                         stan::math::map_rect<1, lp_reduce_functor__>(
                                     ^
./stanExports_negBinomial_MPI.h:1849:12: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
    return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
           ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:129:33: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::model_negBinomial_MPI::log_prob<false, true, double>' requested here
      log_prob = model.template log_prob<false, Jacobian>(unconstrained,
                                ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_negBinomial_MPI_namespace::model_negBinomial_MPI, stan::io::var_context, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
  std::vector<double> cont_vector = util::initialize(
                                          ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_negBinomial_MPI_namespace::model_negBinomial_MPI>' requested here
    return_code = stan::services::diagnose::diagnose(model,
                                            ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_negBinomial_MPI_namespace::model_negBinomial_MPI, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
    ret = command(args, model_, holder, names_oi_tidx_,
          ^
stanExports_negBinomial_MPI.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_negBinomial_MPI_namespace::model_negBinomial_MPI, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>::call_sampler' requested here
    .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
                                                                                      ^
In file included from stanExports_negBinomial_MPI.cc:5:
./stanExports_negBinomial_MPI.h:438:15: warning: unused variable 'global_parameters' [-Wunused-variable]
  const auto& global_parameters = stan::math::to_ref(global_parameters_arg__);
              ^
./stanExports_negBinomial_MPI.h:242:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce<Eigen::Matrix<double, -1, 1, 0>, Eigen::Matrix<stan::math::var_value<double>, -1, 1, 0>, double, nullptr>' requested here
    return lp_reduce(global_parameters, local_parameters, real_data,
           ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_reduce.hpp:68:21: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()<Eigen::Matrix<double, -1, 1, 0>, Eigen::Matrix<stan::math::var_value<double>, -1, 1, 0>, double, nullptr>' requested here
    vector_v fx_v = F()(shared_params, job_specific_params_v, x_r, x_i, msgs);
                    ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:23: note: in instantiation of member function 'stan::math::internal::map_rect_reduce<model_negBinomial_MPI_namespace::lp_reduce_functor__, double, stan::math::var_value<double>>::operator()' requested here
      job_output[i] = ReduceF()(shared_params_dbl, value_of(job_params[i]),
                      ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:183:20: note: in instantiation of function template specialization 'stan::math::internal::map_rect_concurrent<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, const Eigen::Map<Eigen::Matrix<double, -1, 1, 0>, 0> &, stan::math::var_value<double>, nullptr>' requested here
  return internal::map_rect_concurrent<call_id, F, T_shared_param_ref,
                   ^
./stanExports_negBinomial_MPI.h:1246:38: note: in instantiation of function template specialization 'stan::math::map_rect<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, Eigen::Map<Eigen::Matrix<double, -1, 1, 0>, 0>, stan::math::var_value<double>, nullptr>' requested here
                         stan::math::map_rect<1, lp_reduce_functor__>(
                                     ^
./stanExports_negBinomial_MPI.h:1849:12: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
    return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
           ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:167:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model_negBinomial_MPI_namespace::model_negBinomial_MPI>' requested here
      log_prob = stan::model::log_prob_grad<true, Jacobian>(
                              ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_negBinomial_MPI_namespace::model_negBinomial_MPI, stan::io::var_context, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
  std::vector<double> cont_vector = util::initialize(
                                          ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_negBinomial_MPI_namespace::model_negBinomial_MPI>' requested here
    return_code = stan::services::diagnose::diagnose(model,
                                            ^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_negBinomial_MPI_namespace::model_negBinomial_MPI, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
    ret = command(args, model_, holder, names_oi_tidx_,
          ^
stanExports_negBinomial_MPI.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_negBinomial_MPI_namespace::model_negBinomial_MPI, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>::call_sampler' requested here
    .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
                                                                                      ^
8 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ppcseq.so RcppExports.o stanExports_negBinomial_MPI.o -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/Resources/library/00LOCK-ppcseq/00new/ppcseq/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (ppcseq)