Install log for 'rstan'

* installing *source* package ‘rstan’ ...
** package ‘rstan’ 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"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c Module.cpp -o Module.o
In file included from Module.cpp:5:
../inst/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 Module.cpp:5:
../inst/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);
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c chains.cpp -o chains.o
In file included from chains.cpp:19:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/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/4.5/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c init.cpp -o init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c misc.cpp -o misc.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c pointer-tools.cpp -o pointer-tools.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c sparse_extractors.cpp -o sparse_extractors.o
In file included from sparse_extractors.cpp:2:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/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/4.5/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c stan_fit_base.cpp -o stan_fit_base.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c stan_fit_rccp.cpp -o stan_fit_rccp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c version.cpp -o version.o
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 rstan.so Module.o chains.o init.o misc.o pointer-tools.o sparse_extractors.o stan_fit_base.o stan_fit_rccp.o version.o -L/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include' -I/opt/R/arm64/include   -DSTRICT_R_HEADERS -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c stan_fit.cpp -o stan_fit.o
In file included from stan_fit.cpp:20:
../inst/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 stan_fit.cpp:20:
../inst/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 stan_fit.cpp:42:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/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/4.5/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
stan_fit.cpp:1184:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
4 warnings generated.
ar -rs ../inst/lib//libStanServices.a stan_fit.o stan_fit_base.o
ar: creating archive ../inst/lib//libStanServices.a
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.5/rstan.Rcheck/00LOCK-rstan/00new/rstan/libs
** generating debug symbols (dSYM)
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rstan)