* installing *source* package ‘fasttreeid’ ...
** this is package ‘fasttreeid’ version ‘1.0.0’
** package ‘fasttreeid’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.5’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/fasttreeid/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c algebra.cpp -o algebra.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c identification.cpp -o identification.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c random.cpp -o random.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c rbridge.cpp -o rbridge.o
In file included from identification.cpp:1:
In file included from ./identification.h:3:
In file included from ./algebra.h:3:
In file included from ./random.h:3:
In file included from /usr/local/clang21/bin/../include/c++/v1/optional:1312:
In file included from /usr/local/clang21/bin/../include/c++/v1/memory:946:
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:156:81: warning: destructor called on non-final 'fasttreeid::Lambda' 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/clang21/bin/../include/c++/v1/__memory/allocator_traits.h:308:9: note: in instantiation of member function 'std::allocator<fasttreeid::Lambda>::destroy' requested here
308 | __a.destroy(__p);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:181:33: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<fasttreeid::Lambda>>::destroy<fasttreeid::Lambda, 0>' requested here
181 | allocator_traits<_TpAlloc>::destroy(__tmp, __get_elem());
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:184:78: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<fasttreeid::Lambda, std::allocator<fasttreeid::Lambda>>::__on_zero_shared_impl<std::allocator<fasttreeid::Lambda>, 0>' requested here
184 | _LIBCPP_HIDE_FROM_ABI_VIRTUAL void __on_zero_shared() _NOEXCEPT override { __on_zero_shared_impl(); }
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:159:34: note: in instantiation of member function 'std::__shared_ptr_emplace<fasttreeid::Lambda, std::allocator<fasttreeid::Lambda>>::__on_zero_shared' requested here
159 | _LIBCPP_HIDE_FROM_ABI explicit __shared_ptr_emplace(_Alloc __a, _Args&&... __args) : __storage_(std::move(__a)) {
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:736:51: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<fasttreeid::Lambda, std::allocator<fasttreeid::Lambda>>::__shared_ptr_emplace<std::shared_ptr<fasttreeid::RandomTool> &, const unsigned long &, unsigned long &, std::allocator<fasttreeid::Lambda>, 0>' requested here
736 | ::new ((void*)std::addressof(*__guard.__get())) _ControlBlock(__a, std::forward<_Args>(__args)...);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:744:15: note: in instantiation of function template specialization 'std::allocate_shared<fasttreeid::Lambda, std::allocator<fasttreeid::Lambda>, std::shared_ptr<fasttreeid::RandomTool> &, const unsigned long &, unsigned long &, 0>' requested here
744 | return std::allocate_shared<_Tp>(allocator<__remove_cv_t<_Tp> >(), std::forward<_Args>(__args)...);
| ^
identification.cpp:542:37: note: in instantiation of function template specialization 'std::make_shared<fasttreeid::Lambda, std::shared_ptr<fasttreeid::RandomTool> &, const unsigned long &, unsigned long &, 0>' requested here
542 | lambda[directed[i - 1]][i] = std::make_shared<Lambda>(randomTool, directed[i - 1], i);
| ^
/usr/local/clang21/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(); }
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:156:81: warning: destructor called on non-final 'fasttreeid::Omega' 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/clang21/bin/../include/c++/v1/__memory/allocator_traits.h:308:9: note: in instantiation of member function 'std::allocator<fasttreeid::Omega>::destroy' requested here
308 | __a.destroy(__p);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:181:33: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<fasttreeid::Omega>>::destroy<fasttreeid::Omega, 0>' requested here
181 | allocator_traits<_TpAlloc>::destroy(__tmp, __get_elem());
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:184:78: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<fasttreeid::Omega, std::allocator<fasttreeid::Omega>>::__on_zero_shared_impl<std::allocator<fasttreeid::Omega>, 0>' requested here
184 | _LIBCPP_HIDE_FROM_ABI_VIRTUAL void __on_zero_shared() _NOEXCEPT override { __on_zero_shared_impl(); }
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:159:34: note: in instantiation of member function 'std::__shared_ptr_emplace<fasttreeid::Omega, std::allocator<fasttreeid::Omega>>::__on_zero_shared' requested here
159 | _LIBCPP_HIDE_FROM_ABI explicit __shared_ptr_emplace(_Alloc __a, _Args&&... __args) : __storage_(std::move(__a)) {
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:736:51: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<fasttreeid::Omega, std::allocator<fasttreeid::Omega>>::__shared_ptr_emplace<std::shared_ptr<fasttreeid::RandomTool> &, unsigned long &, unsigned long &, std::allocator<fasttreeid::Omega>, 0>' requested here
736 | ::new ((void*)std::addressof(*__guard.__get())) _ControlBlock(__a, std::forward<_Args>(__args)...);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:744:15: note: in instantiation of function template specialization 'std::allocate_shared<fasttreeid::Omega, std::allocator<fasttreeid::Omega>, std::shared_ptr<fasttreeid::RandomTool> &, unsigned long &, unsigned long &, 0>' requested here
744 | return std::allocate_shared<_Tp>(allocator<__remove_cv_t<_Tp> >(), std::forward<_Args>(__args)...);
| ^
identification.cpp:545:22: note: in instantiation of function template specialization 'std::make_shared<fasttreeid::Omega, std::shared_ptr<fasttreeid::RandomTool> &, unsigned long &, unsigned long &, 0>' requested here
545 | omega[u][v] = std::make_shared<Omega>(randomTool, u, v);
| ^
/usr/local/clang21/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(); }
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:156:81: warning: destructor called on non-final 'fasttreeid::Sigma' 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/clang21/bin/../include/c++/v1/__memory/allocator_traits.h:308:9: note: in instantiation of member function 'std::allocator<fasttreeid::Sigma>::destroy' requested here
308 | __a.destroy(__p);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:181:33: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<fasttreeid::Sigma>>::destroy<fasttreeid::Sigma, 0>' requested here
181 | allocator_traits<_TpAlloc>::destroy(__tmp, __get_elem());
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:184:78: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<fasttreeid::Sigma, std::allocator<fasttreeid::Sigma>>::__on_zero_shared_impl<std::allocator<fasttreeid::Sigma>, 0>' requested here
184 | _LIBCPP_HIDE_FROM_ABI_VIRTUAL void __on_zero_shared() _NOEXCEPT override { __on_zero_shared_impl(); }
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:159:34: note: in instantiation of member function 'std::__shared_ptr_emplace<fasttreeid::Sigma, std::allocator<fasttreeid::Sigma>>::__on_zero_shared' requested here
159 | _LIBCPP_HIDE_FROM_ABI explicit __shared_ptr_emplace(_Alloc __a, _Args&&... __args) : __storage_(std::move(__a)) {
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:736:51: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<fasttreeid::Sigma, std::allocator<fasttreeid::Sigma>>::__shared_ptr_emplace<unsigned long &, unsigned long &, std::allocator<fasttreeid::Sigma>, 0>' requested here
736 | ::new ((void*)std::addressof(*__guard.__get())) _ControlBlock(__a, std::forward<_Args>(__args)...);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:744:15: note: in instantiation of function template specialization 'std::allocate_shared<fasttreeid::Sigma, std::allocator<fasttreeid::Sigma>, unsigned long &, unsigned long &, 0>' requested here
744 | return std::allocate_shared<_Tp>(allocator<__remove_cv_t<_Tp> >(), std::forward<_Args>(__args)...);
| ^
identification.cpp:553:23: note: in instantiation of function template specialization 'std::make_shared<fasttreeid::Sigma, unsigned long &, unsigned long &, 0>' requested here
553 | sigma[i][j] = std::make_shared<Sigma>(i, j);
| ^
/usr/local/clang21/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(); }
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o fasttreeid.so RcppExports.o algebra.o identification.o random.o rbridge.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/fasttreeid/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/fasttreeid/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/fasttreeid/src'
installing to /data/gannet/ripley/R/packages/tests-clang/fasttreeid.Rcheck/00LOCK-fasttreeid/00new/fasttreeid/libs
** R
** 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 (fasttreeid)