* installing *source* package ‘spsurv’ ...
** this is package ‘spsurv’ version ‘1.0.0’
** package ‘spsurv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using C++17
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/BH/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include' -I/opt/R/arm64/include -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/BH/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include' -I/opt/R/arm64/include -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_spbp.cc -o stanExports_spbp.o
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/BH/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include' -I/opt/R/arm64/include -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_spbp_frailty.cc -o stanExports_spbp_frailty.o
5 warnings generated.
In file included from stanExports_spbp.cc:5:
In file included from ./stanExports_spbp.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from stanExports_spbp.cc:5:
In file included from ./stanExports_spbp.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from stanExports_spbp.cc:5:
In file included from ./stanExports_spbp.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
47 | virtual std::streamsize xsputn(const char_type* s, int n) {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/streambuf:295:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
295 | virtual streamsize xsputn(const char_type* __s, streamsize __n);
| ^
In file included from stanExports_spbp.cc:5:
In file included from ./stanExports_spbp.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
70 | virtual std::streamsize xsputn(const char_type* s, int n) {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/streambuf:295:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
295 | virtual streamsize xsputn(const char_type* __s, streamsize __n);
| ^
In file included from stanExports_spbp.cc:5:
In file included from ./stanExports_spbp.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from stanExports_spbp.cc:5:
In file included from ./stanExports_spbp.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
In file included from stanExports_spbp_frailty.cc:5:
In file included from ./stanExports_spbp_frailty.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from stanExports_spbp_frailty.cc:5:
In file included from ./stanExports_spbp_frailty.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from stanExports_spbp.cc:5:
In file included from ./stanExports_spbp.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
57 | struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
45 | class ops_partials_edge;
| ^~~~~
| struct
In file included from stanExports_spbp_frailty.cc:5:
In file included from ./stanExports_spbp_frailty.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
47 | virtual std::streamsize xsputn(const char_type* s, int n) {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/streambuf:295:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
295 | virtual streamsize xsputn(const char_type* __s, streamsize __n);
| ^
In file included from stanExports_spbp_frailty.cc:5:
In file included from ./stanExports_spbp_frailty.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:21:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
70 | virtual std::streamsize xsputn(const char_type* s, int n) {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/streambuf:295:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
295 | virtual streamsize xsputn(const char_type* __s, streamsize __n);
| ^
In file included from stanExports_spbp_frailty.cc:5:
In file included from ./stanExports_spbp_frailty.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from stanExports_spbp_frailty.cc:5:
In file included from ./stanExports_spbp_frailty.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
In file included from stanExports_spbp_frailty.cc:5:
In file included from ./stanExports_spbp_frailty.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
57 | struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
45 | class ops_partials_edge;
| ^~~~~
| struct
In file included from stanExports_spbp.cc:5:
In file included from ./stanExports_spbp.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
1252 | int ret = stan::services::error_codes::CONFIG;
| ^
In file included from stanExports_spbp.cc:5:
./stanExports_spbp.h:1674:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
1674 | int pos__ = std::numeric_limits<int>::min();
| ^
In file included from stanExports_spbp_frailty.cc:5:
In file included from ./stanExports_spbp_frailty.h:23:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/rstaninc.hpp:4:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
1252 | int ret = stan::services::error_codes::CONFIG;
| ^
In file included from stanExports_spbp_frailty.cc:5:
./stanExports_spbp_frailty.h:1725:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
1725 | int pos__ = std::numeric_limits<int>::min();
| ^
./stanExports_spbp.h:754:15: warning: unused variable 'b' [-Wunused-variable]
754 | const auto& b = stan::math::to_ref(b_arg__);
| ^
./stanExports_spbp.h:1640:15: note: in instantiation of function template specialization 'model_spbp_namespace::loglik_aft<Eigen::Map<Eigen::Matrix<double, -1, 1>>, Eigen::Matrix<double, -1, 1>, Eigen::Matrix<double, -1, 1>, Eigen::Map<Eigen::Matrix<double, -1, 1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, 1>>, nullptr>' requested here
1640 | loglik_aft(time, beta_scaled, gamma_scaled, status, X, b, B,
| ^
./stanExports_spbp.h:1886:5: note: in instantiation of function template specialization 'model_spbp_namespace::model_spbp::write_array_impl<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>>, std::vector<double>, std::vector<int>, std::vector<double>, nullptr, nullptr, nullptr>' requested here
1886 | write_array_impl(base_rng, params_r, params_i, vars,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/io/random_var_context.hpp:61:11: note: in instantiation of function template specialization 'model_spbp_namespace::model_spbp::write_array<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
61 | model.write_array(rng, unconstrained_params_, int_params,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/services/util/initialize.hpp:94:36: note: in instantiation of function template specialization 'stan::io::random_var_context::random_var_context<model_spbp_namespace::model_spbp, 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
94 | stan::io::random_var_context random_context(model, rng, init_radius,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_spbp_namespace::model_spbp, 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
49 | std::vector<double> cont_vector = util::initialize(
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_spbp_namespace::model_spbp>' requested here
481 | return_code = stan::services::diagnose::diagnose(model,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_spbp_namespace::model_spbp, 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
1215 | ret = command(args, model_, holder, names_oi_tidx_,
| ^
stanExports_spbp.cc:15:79: note: in instantiation of member function 'rstan::stan_fit<model_spbp_namespace::model_spbp, 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
15 | .method("call_sampler", &rstan::stan_fit<stan_model, boost::ecuyer1988> ::call_sampler)
| ^
In file included from stanExports_spbp.cc:5:
./stanExports_spbp.h:755:15: warning: unused variable 'B' [-Wunused-variable]
755 | const auto& B = stan::math::to_ref(B_arg__);
| ^
./stanExports_spbp_frailty.h:781:15: warning: unused variable 'b' [-Wunused-variable]
781 | const auto& b = stan::math::to_ref(b_arg__);
| ^
./stanExports_spbp_frailty.h:1687:15: note: in instantiation of function template specialization 'model_spbp_frailty_namespace::loglik_aft<Eigen::Map<Eigen::Matrix<double, -1, 1>>, Eigen::Matrix<double, -1, 1>, Eigen::Matrix<double, -1, 1>, Eigen::Map<Eigen::Matrix<double, -1, 1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Matrix<double, -1, 1>, nullptr>' requested here
1687 | loglik_aft(time, beta, gamma, status, X, b, B, dist, id, z,
| ^
./stanExports_spbp_frailty.h:1992:5: note: in instantiation of function template specialization 'model_spbp_frailty_namespace::model_spbp_frailty::write_array_impl<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>>, std::vector<double>, std::vector<int>, std::vector<double>, nullptr, nullptr, nullptr>' requested here
1992 | write_array_impl(base_rng, params_r, params_i, vars,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/io/random_var_context.hpp:61:11: note: in instantiation of function template specialization 'model_spbp_frailty_namespace::model_spbp_frailty::write_array<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
61 | model.write_array(rng, unconstrained_params_, int_params,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/services/util/initialize.hpp:94:36: note: in instantiation of function template specialization 'stan::io::random_var_context::random_var_context<model_spbp_frailty_namespace::model_spbp_frailty, 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
94 | stan::io::random_var_context random_context(model, rng, init_radius,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_spbp_frailty_namespace::model_spbp_frailty, 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
49 | std::vector<double> cont_vector = util::initialize(
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_spbp_frailty_namespace::model_spbp_frailty>' requested here
481 | return_code = stan::services::diagnose::diagnose(model,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_spbp_frailty_namespace::model_spbp_frailty, 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
1215 | ret = command(args, model_, holder, names_oi_tidx_,
| ^
stanExports_spbp_frailty.cc:15:79: note: in instantiation of member function 'rstan::stan_fit<model_spbp_frailty_namespace::model_spbp_frailty, 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
15 | .method("call_sampler", &rstan::stan_fit<stan_model, boost::ecuyer1988> ::call_sampler)
| ^
In file included from stanExports_spbp_frailty.cc:5:
./stanExports_spbp_frailty.h:782:15: warning: unused variable 'B' [-Wunused-variable]
782 | const auto& B = stan::math::to_ref(B_arg__);
| ^
./stanExports_spbp.h:754:15: warning: unused variable 'b' [-Wunused-variable]
754 | const auto& b = stan::math::to_ref(b_arg__);
| ^
./stanExports_spbp.h:1460:15: note: in instantiation of function template specialization 'model_spbp_namespace::loglik_aft<Eigen::Map<Eigen::Matrix<double, -1, 1>>, Eigen::Matrix<stan::math::var_value<double>, -1, 1>, Eigen::Matrix<stan::math::var_value<double>, -1, 1>, Eigen::Map<Eigen::Matrix<double, -1, 1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, 1>>, nullptr>' requested here
1460 | loglik_aft(time, beta_scaled, gamma_scaled, status, X, b, B,
| ^
./stanExports_spbp.h:1897:12: note: in instantiation of function template specialization 'model_spbp_namespace::model_spbp::log_prob_impl<true, true, std::vector<stan::math::var_value<double>>, std::vector<int>, nullptr, nullptr>' requested here
1897 | return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_spbp_namespace::model_spbp::log_prob<true, true, stan::math::var_value<double>>' requested here
40 | var adLogProb = model.template log_prob<propto, jacobian_adjust_transform>(
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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_spbp_namespace::model_spbp>' requested here
167 | log_prob = stan::model::log_prob_grad<true, Jacobian>(
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_spbp_namespace::model_spbp, 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
49 | std::vector<double> cont_vector = util::initialize(
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_spbp_namespace::model_spbp>' requested here
481 | return_code = stan::services::diagnose::diagnose(model,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_spbp_namespace::model_spbp, 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
1215 | ret = command(args, model_, holder, names_oi_tidx_,
| ^
stanExports_spbp.cc:15:79: note: in instantiation of member function 'rstan::stan_fit<model_spbp_namespace::model_spbp, 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
15 | .method("call_sampler", &rstan::stan_fit<stan_model, boost::ecuyer1988> ::call_sampler)
| ^
In file included from stanExports_spbp.cc:5:
./stanExports_spbp.h:755:15: warning: unused variable 'B' [-Wunused-variable]
755 | const auto& B = stan::math::to_ref(B_arg__);
| ^
./stanExports_spbp_frailty.h:781:15: warning: unused variable 'b' [-Wunused-variable]
781 | const auto& b = stan::math::to_ref(b_arg__);
| ^
./stanExports_spbp_frailty.h:1405:15: note: in instantiation of function template specialization 'model_spbp_frailty_namespace::loglik_aft<Eigen::Map<Eigen::Matrix<double, -1, 1>>, Eigen::Matrix<stan::math::var_value<double>, -1, 1>, Eigen::Matrix<stan::math::var_value<double>, -1, 1>, Eigen::Map<Eigen::Matrix<double, -1, 1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Map<Eigen::Matrix<double, -1, -1>>, Eigen::Matrix<stan::math::var_value<double>, -1, 1>, nullptr>' requested here
1405 | loglik_aft(time, beta, gamma, status, X, b, B, dist, id, z,
| ^
./stanExports_spbp_frailty.h:2003:12: note: in instantiation of function template specialization 'model_spbp_frailty_namespace::model_spbp_frailty::log_prob_impl<true, true, std::vector<stan::math::var_value<double>>, std::vector<int>, nullptr, nullptr>' requested here
2003 | return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_spbp_frailty_namespace::model_spbp_frailty::log_prob<true, true, stan::math::var_value<double>>' requested here
40 | var adLogProb = model.template log_prob<propto, jacobian_adjust_transform>(
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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_spbp_frailty_namespace::model_spbp_frailty>' requested here
167 | log_prob = stan::model::log_prob_grad<true, Jacobian>(
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_spbp_frailty_namespace::model_spbp_frailty, 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
49 | std::vector<double> cont_vector = util::initialize(
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_spbp_frailty_namespace::model_spbp_frailty>' requested here
481 | return_code = stan::services::diagnose::diagnose(model,
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_spbp_frailty_namespace::model_spbp_frailty, 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
1215 | ret = command(args, model_, holder, names_oi_tidx_,
| ^
stanExports_spbp_frailty.cc:15:79: note: in instantiation of member function 'rstan::stan_fit<model_spbp_frailty_namespace::model_spbp_frailty, 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
15 | .method("call_sampler", &rstan::stan_fit<stan_model, boost::ecuyer1988> ::call_sampler)
| ^
In file included from stanExports_spbp_frailty.cc:5:
./stanExports_spbp_frailty.h:782:15: warning: unused variable 'B' [-Wunused-variable]
782 | const auto& B = stan::math::to_ref(B_arg__);
| ^
14 warnings generated.
14 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 spsurv.so RcppExports.o stanExports_spbp.o stanExports_spbp_frailty.o -L/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/lib -ltbb -ltbbmalloc -L/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/lib/ -Wl,-rpath,/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: ignoring duplicate libraries: '-ltbb', '-ltbbmalloc'
installing to /Volumes/Builds/packages/sonoma-arm64/results/4.6/spsurv.Rcheck/00LOCK-spsurv/00new/spsurv/libs
** generating debug symbols (dSYM)
** R
** 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 (spsurv)