Install log for 'glmmrBase'

* installing *source* package ‘glmmrBase’ ...
** package ‘glmmrBase’ successfully unpacked and MD5 sums checked
** using staged installation
Warning message:
In .warning_nowrite(file.path(basename(pkgdir), ...)) :
  'glmmrBase/src/Makevars' already exists.  Not overwritten by rstantools.FALSE
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++17
using SDK: ‘MacOSX11.3.sdk’


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c heckman.cpp -o heckman.o


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c model_module.cpp -o model_module.o
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c stanExports_mcml.cc -o stanExports_mcml.o
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
../inst/include/glmmr/general.h:19:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined]
#define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
        ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here
#define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
        ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:34:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/SparseChol.h:3:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/sparsematrix.h:145:7: warning: unused variable 'x' [-Wunused-variable]
  int x ;
      ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/sparsematrix.h:437:10: warning: unused variable 'val' [-Wunused-variable]
  double val;
         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/sparsematrix.h:647:10: warning: unused variable 'mem' [-Wunused-variable]
  double mem = 0;
         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/sparsematrix.h:648:7: warning: unused variable 'nz' [-Wunused-variable]
  int nz = Ap.back();
      ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/sparsematrix.h:809:7: warning: variable 'ncmpa' set but not used [-Wunused-but-set-variable]
  int ncmpa = 0 ;
      ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/sparsematrix.h:837:19: warning: unused variable 'ilast' [-Wunused-variable]
  int deg, inext, ilast;
                  ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:34:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/SparseChol.h:4:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/SparseChol/include/operators.h:14:10: warning: unused variable 'val' [-Wunused-variable]
  double val;
         ^
In file included from stanExports_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from stanExports_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from stanExports_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from stanExports_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:6:
In file included from ../inst/include/glmmr/formula.hpp:6:
../inst/include/glmmr/formulaparse.h:12:11: warning: unused variable 'a' [-Wunused-variable]
    float a = std::stod(s);
          ^
../inst/include/glmmr/formulaparse.h:223:19: warning: variable 'variable_in_data' set but not used [-Wunused-but-set-variable]
  bool add_check, variable_in_data;
                  ^
In file included from stanExports_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
5 warnings generated.
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:9:
In file included from ../inst/include/glmmr/model.hpp:4:
In file included from ../inst/include/glmmr/modelbits.hpp:6:
../inst/include/glmmr/nngpcovariance.hpp:379:14: warning: unused variable 'av' [-Wunused-variable]
  double au, av, qf;
             ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:9:
In file included from ../inst/include/glmmr/model.hpp:8:
In file included from ../inst/include/glmmr/modeloptim.hpp:12:
../inst/include/glmmr/optim/optim.h:354:12: warning: unused variable 'result' [-Wunused-variable]
    double result = newuoa_closure( &closure, dim, control.npt, current_values.data(), control.rhobeg, control.rhoend, control.maxfun, w.data(), &fn_counter);
           ^
../inst/include/glmmr/optim/optim.h:503:16: warning: unused variable 'a' [-Wunused-variable]
        double a = eval(current_values, g);
               ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:9:
In file included from ../inst/include/glmmr/model.hpp:8:
../inst/include/glmmr/modeloptim.hpp:754:12: warning: variable 'trCZZD' set but not used [-Wunused-but-set-variable]
    double trCZZD, trCZZ;
           ^
model_module.cpp:2216:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
     int a, b; // needed for defines on machines without openmp
         ^
In file included from stanExports_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:4:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_mcml.cc:5:
./stanExports_mcml.h:664:20: warning: unused variable 'jacobian__' [-Wunused-variable]
    constexpr bool jacobian__ = false;
                   ^
./stanExports_mcml.h:701:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
./stanExports_mcml.h:727:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
In file included from stanExports_mcml.cc:5:
In file included from ./stanExports_mcml.h:23:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/math/special_functions/beta.hpp:1721:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable]
      const T x_extrema = 1 / (1 + a);
              ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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-x86_64/Rlib/4.3/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::overflow_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-x86_64/Rlib/4.3/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::overflow_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-x86_64/Rlib/4.3/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-x86_64/Rlib/4.3/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 model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/RcppEigen.h:26:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp.h:46:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::nngpCovariance, glmmr::LinearPredictor>>>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Model<glmmr::ModelBits<glmmr::hsgpCovariance, glmmr::LinearPredictor>>>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::LinearPredictor' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::LinearPredictor>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::Covariance' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::Covariance>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::nngpCovariance' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::nngpCovariance>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::hsgpCovariance' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::hsgpCovariance>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:31:5: warning: delete called on non-final 'glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<glmmr::ModelBits<glmmr::Covariance, glmmr::LinearPredictor>>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:9:
In file included from ../inst/include/glmmr/model.hpp:8:
In file included from ../inst/include/glmmr/modeloptim.hpp:12:
../inst/include/glmmr/optim/optim.h:413:20: warning: private field 'iter' is not used [-Wunused-private-field]
  int              iter = 0;
                   ^
13 warnings generated.
29 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o glmmrBase.so RcppExports.o heckman.o model_module.o stanExports_mcml.o -L/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/lib -ltbb -ltbbmalloc -L/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/lib/ -Wl,-rpath,/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppParallel/lib/ -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/Volumes/Builds/packages/big-sur-x86_64/results/4.3/glmmrBase.Rcheck/00_pkg_src/glmmrBase/src/heckman.o: no symbols
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/glmmrBase.Rcheck/00LOCK-glmmrBase/00new/glmmrBase/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (glmmrBase)