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jtimonen / lgpr

R-package for interpretable nonparametric modeling of longitudinal data using additive Gaussian processes. Contains functionality for inferring covariate effects and assessing covariate relevances. Various models can be specified using a convenient formula syntax.
https://jtimonen.github.io/lgpr-usage/
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Build failure on macOS in Macports (clang/gcc): error: cannot initialize a member subobject of type 'std::ostream *' with an lvalue of type 'SEXP' (aka 'SEXPREC *') #27

Closed barracuda156 closed 1 year ago

barracuda156 commented 1 year ago 
In file included from RcppExports.cpp:4:
  In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
  In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:26:
  In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:169:
  In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/as.h:25:
  /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:31:28: error: cannot initialize a member subobject of type 'std::ostream *' with an lvalue of type 'SEXP' (aka 'SEXPREC *')
                      Exporter( SEXP x ) : t(x){}
                                           ^ ~
  /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/as.h:87:41: note: in instantiation of member function 'Rcpp::traits::Exporter<std::ostream *>::Exporter' requested here
              ::Rcpp::traits::Exporter<T> exporter(x);
                                          ^
  /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/as.h:152:26: note: in instantiation of function template specialization 'Rcpp::internal::as<std::ostream *>' requested here
          return internal::as<T>(x, typename traits::r_type_traits<T>::r_category());
                           ^
  /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/InputParameter.h:34:38: note: in instantiation of function template specialization 'Rcpp::as<std::ostream *>' requested here
          inline operator T() { return as<T>(x) ; }
                                       ^
  RcppExports.cpp:23:54: note: in instantiation of member function 'Rcpp::InputParameter<std::ostream *>::operator std::ostream *' requested here
      rcpp_result_gen = Rcpp::wrap(STAN_var_mask(x, a, pstream__));
                                                       ^
  18 warnings and 1 error generated.

gcc-12 builds it fine, but clang-15 fails. Complete log can be found at: https://github.com/macports/macports-ports/actions/runs/4634085782/jobs/8199927979?pr=18211

jtimonen commented 1 year ago

@andrjohns any idea what this is?

andrjohns commented 1 year ago

@barracuda156 this is more likely an issue with the ported toolchain/packages, rather than lgpr, since lgpr builds under all CRAN machines, including one with Clang 15

barracuda156 commented 1 year ago

@barracuda156 this is more likely an issue with the ported toolchain/packages, rather than lgpr, since lgpr builds under all CRAN machines, including one with Clang 15

@andrjohns The same package builds fine in Macports environment with GCC for MacOS PowerPC. So environment is not to blame, IMO.

andrjohns commented 1 year ago

Right, but if the package builds in all environments except for your custom toolchain, then it's not likely to be the package. If you can replicate the error with a toolchain other than the macports clang-15, then I'd be able to debug, but there's not much else that I can do

barracuda156 commented 1 year ago

Right, but if the package builds in all environments except for your custom toolchain, then it's not likely to be the package. If you can replicate the error with a toolchain other than the macports clang-15, then I'd be able to debug, but there's not much else that I can do

@andrjohns Thank you for responding. I will try.

Generally speaking, Macports toolchain and R are perfectly fine on x86_64/aarch64 (i386/ppc/ppc64 may indeed have issues, since not many people work on supporting them). But I do not know the cause of this specific error.

barracuda156 commented 1 year ago

@andrjohns Interestingly, I got it now with gcc as well:

* installing *source* package ‘lgpr’ ...
** using staged installation
** libs

/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -pipe -Os -arch ppc  -c RcppExports.cpp -o RcppExports.o
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:428,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/as.h:25,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:169,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:26:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h: In instantiation of 'Rcpp::traits::Exporter<T>::Exporter(SEXP) [with T = std::basic_ostream<char>*; SEXP = SEXPREC*]':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/as.h:87:41:   required from 'T Rcpp::internal::as(SEXP, Rcpp::traits::r_type_generic_tag) [with T = std::basic_ostream<char>*; SEXP = SEXPREC*]'
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/as.h:152:31:   required from 'T Rcpp::as(SEXP) [with T = std::basic_ostream<char>*; SEXP = SEXPREC*]'
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/InputParameter.h:34:43:   required from 'Rcpp::InputParameter<T>::operator T() [with T = std::basic_ostream<char>*]'
RcppExports.cpp:23:47:   required from here
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:31:44: error: cannot convert 'SEXP' {aka 'SEXPREC*'} to 'std::basic_ostream<char>*' in initialization
   31 |                     Exporter( SEXP x ) : t(x){}
      |                                            ^
      |                                            |
      |                                            SEXP {aka SEXPREC*}
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:67,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
/opt/local/Library/Frameworks/R.framework/Resources/include/Rinternals.h:180:16: note: class type 'SEXPREC' is incomplete
  180 | typedef struct SEXPREC *SEXP;
      |                ^~~~~~~
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘lgpr’

But it does not happen when I run testing – i.e. with R CHECK it builds fine! Weird. Everything else is the same (compiler, packages versions etc.)

* installing *source* package ‘lgpr’ ...
** using staged installation
** libs

/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -pipe -Os -arch ppc  -c RcppExports.cpp -o RcppExports.o
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:428,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from lgpr_types.h:2,
                 from RcppExports.cpp:4:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~

/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -pipe -Os -arch ppc  -c exports.stanfunctions.cpp -o exports.stanfunctions.o
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:428,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from exports.stanfunctions.cpp:8:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/shared_ptr.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:7,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math.hpp:4,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from exports.stanfunctions.cpp:12:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/detail/shared_count.hpp: At global scope:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /opt/local/include/gcc12/c++/memory:76,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include/tbb/tbb_stddef.h:431,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include/tbb/tbb_machine.h:113,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include/tbb/atomic.h:28,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include/tbb/task_scheduler_observer.h:20,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/init_chainablestack.hpp:8,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:8,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/traits.hpp:21,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/storage.hpp:27,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:336:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp: At global scope:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  111 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
In file included from /opt/local/include/gcc12/c++/bits/stl_algobase.h:65,
                 from /opt/local/include/gcc12/c++/bits/specfun.h:45,
                 from /opt/local/include/gcc12/c++/cmath:1935,
                 from /opt/local/include/LegacySupport/cmath:54,
                 from /opt/local/include/gcc12/c++/complex:44,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:96:
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  149 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~

/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -pipe -Os -arch ppc  -c stanExports_lgp.cc -o stanExports_lgp.o
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:428,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stanExports_lgp.h:6,
                 from stanExports_lgp.cc:5:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/shared_ptr.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/detail/shared_count.hpp: At global scope:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /opt/local/include/gcc12/c++/memory:76,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:7:
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/traits.hpp:21,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/storage.hpp:27,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp: At global scope:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  111 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
In file included from /opt/local/include/gcc12/c++/bits/stl_algobase.h:65,
                 from /opt/local/include/gcc12/c++/bits/specfun.h:45,
                 from /opt/local/include/gcc12/c++/cmath:1935,
                 from /opt/local/include/LegacySupport/cmath:54,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_lgp.cc:3:
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  149 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~

/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -pipe -Os -arch ppc  -c stanExports_lgp_latent.cc -o stanExports_lgp_latent.o
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:428,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stanExports_lgp_latent.h:6,
                 from stanExports_lgp_latent.cc:5:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/shared_ptr.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/detail/shared_count.hpp: At global scope:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /opt/local/include/gcc12/c++/memory:76,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:7:
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/traits.hpp:21,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/storage.hpp:27,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp: At global scope:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  111 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
In file included from /opt/local/include/gcc12/c++/bits/stl_algobase.h:65,
                 from /opt/local/include/gcc12/c++/bits/specfun.h:45,
                 from /opt/local/include/gcc12/c++/cmath:1935,
                 from /opt/local/include/LegacySupport/cmath:54,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_lgp_latent.cc:3:
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  149 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~

/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -I'/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -pipe -Os -arch ppc  -c stanExports_parameter_prior.cc -o stanExports_parameter_prior.o
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:428,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stanExports_parameter_prior.h:6,
                 from stanExports_parameter_prior.cc:5:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h: In constructor 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:20: warning: 'Eigen::internal::scalar_sum_op<bool, bool>::scalar_sum_op()' is deprecated [-Wdeprecated-declarations]
   66 |   scalar_sum_op() {}
      |                    ^
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:66:3: note: declared here
   66 |   scalar_sum_op() {}
      |   ^~~~~~~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/shared_ptr.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/detail/shared_count.hpp: At global scope:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /opt/local/include/gcc12/c++/memory:76,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:7:
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/traits.hpp:21,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/storage.hpp:27,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp: At global scope:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  111 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
In file included from /opt/local/include/gcc12/c++/bits/stl_algobase.h:65,
                 from /opt/local/include/gcc12/c++/bits/specfun.h:45,
                 from /opt/local/include/gcc12/c++/cmath:1935,
                 from /opt/local/include/LegacySupport/cmath:54,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_parameter_prior.cc:3:
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  149 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
/opt/local/include/gcc12/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33:
/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
/opt/local/include/gcc12/c++/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/local/bin/g++-mp-12 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -L/opt/local/lib -lMacportsLegacySupport -arch ppc -o lgpr.so RcppExports.o exports.stanfunctions.o stanExports_lgp.o stanExports_lgp_latent.o stanExports_parameter_prior.o -L/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/lib/ -Wl,-rpath,/opt/local/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /opt/local/var/macports/build/_opt_PPCRosettaPorts_R_R-lgpr/R-lgpr/work/lgpr-1.2.3/lgpr.Rcheck/00LOCK-lgpr/00new/lgpr/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (lgpr)

Any idea why this could be the case?

andrjohns commented 1 year ago

Given that this is only occurring with the macports compilers, the likely cause would be something to do with how they've been patched/configured from the vanilla clang/gcc. If g++-12 works without issue, but g++-mp-12 does not, then it's going to be a macports issue.

barracuda156 commented 1 year ago

Given that this is only occurring with the macports compilers, the likely cause would be something to do with how they've been patched/configured from the vanilla clang/gcc. If g++-12 works without issue, but g++-mp-12 does not, then it's going to be a macports issue.

@andrjohns In both cases it is Macports compiler – moreover, it is identical, literally (same machine, everything is identical). I ran tests first, and build is okay, then wanted to install, and build failed.

UPD. Since the error occurs both with gcc12 (locally) and clang (Macports buildbots), it is not compiler-specific. Also, it is the only case of such an error I have seen so far – and we built over 1500 packages by now, many of which are Rcpp-based.

andrjohns commented 1 year ago

In both cases it is Macports compiler – moreover, it is identical, literally (same machine, everything is identical). I ran tests first, and build is okay, then wanted to install, and build failed.

Yes, but the error/behaviour does not occur outside of Macports - the same versions of clang/gcc, R, and lgpr work without issue across Windows, Linux, and MacOS. This isn't something that anyone else can really debug, since it's only occurring in your specific environment and configuration

barracuda156 commented 1 year ago

In both cases it is Macports compiler – moreover, it is identical, literally (same machine, everything is identical). I ran tests first, and build is okay, then wanted to install, and build failed.

Yes, but the error/behaviour does not occur outside of Macports - the same versions of clang/gcc, R, and lgpr work without issue across Windows, Linux, and MacOS. This isn't something that anyone else can really debug, since it's only occurring in your specific environment and configuration

@andrjohns Well, if you could install it in Macports, it will be debuggable – and on x86/aarch64 you won’t need to build everything from scratch, only lgpr itself. Everything else Macports will install pre-built.

andrjohns commented 1 year ago

Do you get the same behaviour/error on x86_64? Your logs above are both for ppc

barracuda156 commented 1 year ago

Do you get the same behaviour/error on x86_64? Your logs above are both for ppc

Yes, otherwise I would have explicitly made clear the error is PPC-specific. Original report above has the link to Intel log: https://github.com/macports/macports-ports/actions/runs/4634085782/jobs/8199927979?pr=18211#step:8:18537

Portfile for lgpr: https://github.com/barracuda156/macports-ports/blob/lgpr/R/R-lgpr/Portfile

andrjohns commented 1 year ago

In that case, it does seem like some part of the porting process is the likely culprit - whether it's the ported R, toolchain, or package (or dependencies), since there are no issues for x86_64 outside of macports.

barracuda156 commented 1 year ago

In that case, it does seem like some part of the porting process is the likely culprit - whether it's the ported R, toolchain, or package (or dependencies), since there are no issues for x86_64 outside of macports.

Well, there are numerous variables, so it is never possible to rule out something influencing something else, but at the same time this is the only single failure of this kind out of 1500+ R packages in Macports, built with the same toolchain etc.

UPD. Out of 2800 R packages :)

barracuda156 commented 1 year ago

@jtimonen @andrjohns While these errors were apparently ignored for quite a while, new version (1.2.4) builds fine for me with gcc. Still need to verify clangs builds are also okay.

barracuda156 commented 1 year ago

UPD. Yes, 1.2.4 confirmed to build fine both with Clang on new macOS and with GCC on 10.6 for PowerPC: https://github.com/macports/macports-ports/pull/20561 Closing the issue.

jtimonen commented 1 year ago

Thanks, that is good news