* installing *source* package ‘dynsurv’ ...
** this is package ‘dynsurv’ version ‘0.4-7’
** package ‘dynsurv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 20.1.0-rc2’
using C++ compiler: ‘clang version 20.1.0-rc2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/dynsurv/src'
/usr/local/clang20/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -I. -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c IntRegPar.cpp -o IntRegPar.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 /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/config.hpp:48:
/data/gannet/ripley/R/test-clang/BH/include/boost/config/stdlib/libcpp.hpp:98:11: warning: 'BOOST_NO_AUTO_PTR' macro redefined [-Wmacro-redefined]
98 | # define BOOST_NO_AUTO_PTR
| ^
<command line>:3:9: note: previous definition is here
3 | #define BOOST_NO_AUTO_PTR 1
| ^
/usr/local/clang20/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c arms.c -o arms.o
1 warning generated.
/usr/local/clang20/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -I. -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c bayesCox.cpp -o bayesCox.o
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 /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/config.hpp:48:
/data/gannet/ripley/R/test-clang/BH/include/boost/config/stdlib/libcpp.hpp:98:11: warning: 'BOOST_NO_AUTO_PTR' macro redefined [-Wmacro-redefined]
98 | # define BOOST_NO_AUTO_PTR
| ^
<command line>:3:9: note: previous definition is here
3 | #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]
65 | 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]
85 | int err;
| ^
./TimeVaryingModel.h:162:7: warning: variable 'err' set but not used [-Wunused-but-set-variable]
162 | 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]
355 | int err;
| ^
./DynamicModel.h:452:11: warning: variable 'err' set but not used [-Wunused-but-set-variable]
452 | 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>, ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:48:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::shared_ptr<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>' requested here
48 | boost::shared_ptr<M> 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 /usr/local/clang20/bin/../include/c++/v1/iostream:45:
In file included from /usr/local/clang20/bin/../include/c++/v1/ios:223:
In file included from /usr/local/clang20/bin/../include/c++/v1/__locale:24:
In file included from /usr/local/clang20/bin/../include/c++/v1/string:611:
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator.h:156:81: warning: destructor called on non-final 'ir::TimeIndepCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
156 | _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
| ^
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator_traits.h:324:9: note: in instantiation of member function 'std::allocator<ir::TimeIndepCoxPar>::destroy' requested here
324 | __a.destroy(__p);
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:749:23: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<ir::TimeIndepCoxPar>>::destroy<ir::TimeIndepCoxPar, 0>' requested here
749 | __alloc_traits::destroy(this->__alloc_, std::__to_address(--__soon_to_be_end));
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:531:5: note: in instantiation of member function 'std::vector<ir::TimeIndepCoxPar>::__base_destruct_at_end' requested here
531 | __base_destruct_at_end(this->__begin_);
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:248:16: note: in instantiation of member function 'std::vector<ir::TimeIndepCoxPar>::clear' requested here
248 | __vec_.clear();
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:259:67: note: in instantiation of member function 'std::vector<ir::TimeIndepCoxPar>::__destroy_vector::operator()' requested here
259 | _LIBCPP_CONSTEXPR_SINCE_CXX20 _LIBCPP_HIDE_FROM_ABI ~vector() { __destroy_vector (*this)(); }
| ^
./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector<ir::TimeIndepCoxPar>::~vector' requested here
40 | GibbsSampler(const boost::shared_ptr<M>& pm,
| ^
bayesCox.cpp:50:23: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::GibbsSampler' requested here
50 | GibbsSampler<M> gs(pm, p_iter[0]);
| ^
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator.h:156:87: note: qualify call to silence this warning
156 | _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>, ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:76:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>::shared_ptr<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>' requested here
76 | boost::shared_ptr<M> 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>, ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:104:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
104 | boost::shared_ptr<M> 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 /usr/local/clang20/bin/../include/c++/v1/iostream:45:
In file included from /usr/local/clang20/bin/../include/c++/v1/ios:223:
In file included from /usr/local/clang20/bin/../include/c++/v1/__locale:24:
In file included from /usr/local/clang20/bin/../include/c++/v1/string:611:
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator.h:156:81: warning: destructor called on non-final 'ir::TimeVaryingCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
156 | _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
| ^
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator_traits.h:324:9: note: in instantiation of member function 'std::allocator<ir::TimeVaryingCoxPar>::destroy' requested here
324 | __a.destroy(__p);
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:749:23: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<ir::TimeVaryingCoxPar>>::destroy<ir::TimeVaryingCoxPar, 0>' requested here
749 | __alloc_traits::destroy(this->__alloc_, std::__to_address(--__soon_to_be_end));
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:531:5: note: in instantiation of member function 'std::vector<ir::TimeVaryingCoxPar>::__base_destruct_at_end' requested here
531 | __base_destruct_at_end(this->__begin_);
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:248:16: note: in instantiation of member function 'std::vector<ir::TimeVaryingCoxPar>::clear' requested here
248 | __vec_.clear();
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:259:67: note: in instantiation of member function 'std::vector<ir::TimeVaryingCoxPar>::__destroy_vector::operator()' requested here
259 | _LIBCPP_CONSTEXPR_SINCE_CXX20 _LIBCPP_HIDE_FROM_ABI ~vector() { __destroy_vector (*this)(); }
| ^
./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector<ir::TimeVaryingCoxPar>::~vector' requested here
40 | GibbsSampler(const boost::shared_ptr<M>& pm,
| ^
bayesCox.cpp:107:23: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>::GibbsSampler' requested here
107 | GibbsSampler<M> gs(pm, p_iter[0]);
| ^
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator.h:156:87: note: qualify call to silence this warning
156 | _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>, ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:133:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
133 | boost::shared_ptr<M> 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>, ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:164:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
164 | boost::shared_ptr<M> 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>, ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:193:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
193 | boost::shared_ptr<M> 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>, ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:224:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
224 | boost::shared_ptr<M> 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 /usr/local/clang20/bin/../include/c++/v1/iostream:45:
In file included from /usr/local/clang20/bin/../include/c++/v1/ios:223:
In file included from /usr/local/clang20/bin/../include/c++/v1/__locale:24:
In file included from /usr/local/clang20/bin/../include/c++/v1/string:611:
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator.h:156:81: warning: destructor called on non-final 'ir::DynamicCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
156 | _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
| ^
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator_traits.h:324:9: note: in instantiation of member function 'std::allocator<ir::DynamicCoxPar>::destroy' requested here
324 | __a.destroy(__p);
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:749:23: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<ir::DynamicCoxPar>>::destroy<ir::DynamicCoxPar, 0>' requested here
749 | __alloc_traits::destroy(this->__alloc_, std::__to_address(--__soon_to_be_end));
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:531:5: note: in instantiation of member function 'std::vector<ir::DynamicCoxPar>::__base_destruct_at_end' requested here
531 | __base_destruct_at_end(this->__begin_);
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:248:16: note: in instantiation of member function 'std::vector<ir::DynamicCoxPar>::clear' requested here
248 | __vec_.clear();
| ^
/usr/local/clang20/bin/../include/c++/v1/__vector/vector.h:259:67: note: in instantiation of member function 'std::vector<ir::DynamicCoxPar>::__destroy_vector::operator()' requested here
259 | _LIBCPP_CONSTEXPR_SINCE_CXX20 _LIBCPP_HIDE_FROM_ABI ~vector() { __destroy_vector (*this)(); }
| ^
./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector<ir::DynamicCoxPar>::~vector' requested here
40 | GibbsSampler(const boost::shared_ptr<M>& pm,
| ^
bayesCox.cpp:228:23: note: in instantiation of member function 'ir::GibbsSampler<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>::GibbsSampler' requested here
228 | GibbsSampler<M> gs(pm, p_iter[0]);
| ^
/usr/local/clang20/bin/../include/c++/v1/__memory/allocator.h:156:87: note: qualify call to silence this warning
156 | _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>, ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:257:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
257 | boost::shared_ptr<M> 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>, ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:292:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>::shared_ptr<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>' requested here
292 | boost::shared_ptr<M> 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>, ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:324:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>' requested here
324 | boost::shared_ptr<M> 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>, ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:359:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
359 | boost::shared_ptr<M> 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 /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
44 | delete x;
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
150 | boost::checked_delete( p );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:205:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
205 | boost::detail::shared_count( p ).swap( pn );
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:283:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>, ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ^
bayesCox.cpp:392:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
392 | boost::shared_ptr<M> pm(new M(pd));
| ^
/usr/local/clang20/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c dynsurv_init.c -o dynsurv_init.o
21 warnings generated.
/usr/local/clang20/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang20/lib -L/usr/local/clang20/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o dynsurv.so IntRegPar.o arms.o bayesCox.o dynsurv_init.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/dynsurv/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/dynsurv/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/dynsurv/src'
installing to /data/gannet/ripley/R/packages/tests-clang/dynsurv.Rcheck/00LOCK-dynsurv/00new/dynsurv/libs
** 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)