Install log for 'LMMELSM'

* installing *source* package ‘LMMELSM’ ...
** package ‘LMMELSM’ successfully unpacked and MD5 sums checked
** 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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/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'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include    -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/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'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include    -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_lmmelsmPred.cc -o stanExports_lmmelsmPred.o
In file included from stanExports_lmmelsmPred.cc:5:
In file included from ./stanExports_lmmelsmPred.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<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_lmmelsmPred.cc:5:
In file included from ./stanExports_lmmelsmPred.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<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_lmmelsmPred.cc:5:
In file included from ./stanExports_lmmelsmPred.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_lmmelsmPred.cc:5:
In file included from ./stanExports_lmmelsmPred.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_lmmelsmPred.cc:5:
./stanExports_lmmelsmPred.h:2162:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
In file included from stanExports_lmmelsmPred.cc:5:
In file included from ./stanExports_lmmelsmPred.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/beta.hpp:1721:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable]
      const T x_extrema = 1 / (1 + a);
              ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
      temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
      ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<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);
                   ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<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(
                ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<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);
          ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<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<>());
                      ^
6 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/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'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include    -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_lmmelsmPredObs2.cc -o stanExports_lmmelsmPredObs2.o
In file included from stanExports_lmmelsmPredObs2.cc:5:
In file included from ./stanExports_lmmelsmPredObs2.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<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_lmmelsmPredObs2.cc:5:
In file included from ./stanExports_lmmelsmPredObs2.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<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_lmmelsmPredObs2.cc:5:
In file included from ./stanExports_lmmelsmPredObs2.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_lmmelsmPredObs2.cc:5:
In file included from ./stanExports_lmmelsmPredObs2.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_lmmelsmPredObs2.cc:5:
./stanExports_lmmelsmPredObs2.h:2011:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
In file included from stanExports_lmmelsmPredObs2.cc:5:
In file included from ./stanExports_lmmelsmPredObs2.h:23:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/beta.hpp:1721:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable]
      const T x_extrema = 1 / (1 + a);
              ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
      temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
      ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<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);
                   ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<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(
                ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<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);
          ^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<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<>());
                      ^
6 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 LMMELSM.so RcppExports.o stanExports_lmmelsmPred.o stanExports_lmmelsmPredObs2.o -L/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib/ -Wl,-rpath,/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/LMMELSM.Rcheck/00LOCK-LMMELSM/00new/LMMELSM/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LMMELSM)