* installing *source* package ‘dynsurv’ ... ** package ‘dynsurv’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I/opt/R/x86_64/include -I. -fPIC -falign-functions=64 -Wall -g -O2 -c IntRegPar.cpp -o IntRegPar.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c arms.c -o arms.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I/opt/R/x86_64/include -I. -fPIC -falign-functions=64 -Wall -g -O2 -c bayesCox.cpp -o bayesCox.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dynsurv_init.c -o dynsurv_init.o In file included from IntRegPar.cpp:10: In file included from ./IntRegPar.h:15: In file included from ./ublas.h:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/numeric/ublas/vector.hpp:20: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/config.hpp:48: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/config/stdlib/libcpp.hpp:98:11: warning: 'BOOST_NO_AUTO_PTR' macro redefined [-Wmacro-redefined] # define BOOST_NO_AUTO_PTR ^ :3:9: note: previous definition is here #define BOOST_NO_AUTO_PTR 1 ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:16: In file included from ./IntRegPar.h:15: In file included from ./ublas.h:14: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/numeric/ublas/vector.hpp:20: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/config.hpp:48: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/config/stdlib/libcpp.hpp:98:11: warning: 'BOOST_NO_AUTO_PTR' macro redefined [-Wmacro-redefined] # define BOOST_NO_AUTO_PTR ^ :3:9: note: previous definition is here #define BOOST_NO_AUTO_PTR 1 ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: ./TimeIndepModel.h:65:7: warning: variable 'err' set but not used [-Wunused-but-set-variable] int err; ^ In file included from bayesCox.cpp:4: In file included from ./TimeVaryingCoxModel.h:17: ./TimeVaryingModel.h:85:7: warning: variable 'err' set but not used [-Wunused-but-set-variable] int err; ^ ./TimeVaryingModel.h:162:7: warning: variable 'err' set but not used [-Wunused-but-set-variable] int err; ^ In file included from bayesCox.cpp:5: In file included from ./DynamicCoxModel.h:17: ./DynamicModel.h:355:11: warning: variable 'err' set but not used [-Wunused-but-set-variable] int err; ^ ./DynamicModel.h:452:11: warning: variable 'err' set but not used [-Wunused-but-set-variable] int err; ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::TimeIndepCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::TimeIndepCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:48:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:15: In file included from ./IntRegPrior.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/iostream:37: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string_view:175: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__string:57: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:86: warning: destructor called on non-final 'ir::TimeIndepCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator::destroy' requested here __a.destroy(__p); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits>::__destroy' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits>::destroy' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base>::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base>::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:497:5: note: in instantiation of member function 'std::__vector_base>::~__vector_base' requested here vector() _NOEXCEPT_(is_nothrow_default_constructible::value) ^ ./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector::vector' requested here GibbsSampler(const boost::shared_ptr& pm, ^ bayesCox.cpp:50:23: note: in instantiation of member function 'ir::GibbsSampler>>::GibbsSampler' requested here GibbsSampler gs(pm, p_iter[0]); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: qualify call to silence this warning _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::TimeIndepCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::TimeIndepCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:76:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::TimeVaryingCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:104:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:15: In file included from ./IntRegPrior.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/iostream:37: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string_view:175: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__string:57: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:86: warning: destructor called on non-final 'ir::TimeVaryingCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator::destroy' requested here __a.destroy(__p); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits>::__destroy' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits>::destroy' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base>::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base>::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:497:5: note: in instantiation of member function 'std::__vector_base>::~__vector_base' requested here vector() _NOEXCEPT_(is_nothrow_default_constructible::value) ^ ./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector::vector' requested here GibbsSampler(const boost::shared_ptr& pm, ^ bayesCox.cpp:107:23: note: in instantiation of member function 'ir::GibbsSampler>>::GibbsSampler' requested here GibbsSampler gs(pm, p_iter[0]); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: qualify call to silence this warning _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::TimeVaryingCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:133:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::TimeVaryingCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:164:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::TimeVaryingCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:193:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::DynamicCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::DynamicCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:224:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:15: In file included from ./IntRegPrior.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/iostream:37: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string_view:175: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__string:57: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:86: warning: destructor called on non-final 'ir::DynamicCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator::destroy' requested here __a.destroy(__p); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits>::__destroy' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits>::destroy' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base>::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base>::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:497:5: note: in instantiation of member function 'std::__vector_base>::~__vector_base' requested here vector() _NOEXCEPT_(is_nothrow_default_constructible::value) ^ ./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector::vector' requested here GibbsSampler(const boost::shared_ptr& pm, ^ bayesCox.cpp:228:23: note: in instantiation of member function 'ir::GibbsSampler>>::GibbsSampler' requested here GibbsSampler gs(pm, p_iter[0]); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: qualify call to silence this warning _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::DynamicCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::DynamicCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:257:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ 1 warning generated. In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::DynamicCoxModel_v2>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::DynamicCoxModel_v2>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:292:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::DynamicCoxModel_v2>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::DynamicCoxModel_v2>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:324:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::DynamicCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::DynamicCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:359:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ In file included from bayesCox.cpp:3: In file included from ./TimeIndepCoxModel.h:17: In file included from ./TimeIndepModel.h:15: In file included from ./IntRegModel.h:18: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:17: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'ir::DynamicCoxModel>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete>>' requested here boost::checked_delete( p ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:279:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count>>' requested here boost::detail::shared_count( p ).swap( pn ); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:373:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct>, ir::DynamicCoxModel>>' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ bayesCox.cpp:392:28: note: in instantiation of function template specialization 'boost::shared_ptr>>::shared_ptr>>' requested here boost::shared_ptr pm(new M(pd)); ^ 21 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o dynsurv.so IntRegPar.o arms.o bayesCox.o dynsurv_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/dynsurv.Rcheck/00LOCK-dynsurv/00new/dynsurv/libs ** generating debug symbols (dSYM) ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dynsurv)