* installing *source* package ‘fasttreeid’ ... ** this is package ‘fasttreeid’ version ‘1.0.1’ ** package ‘fasttreeid’ successfully unpacked and MD5 sums checked ** using staged installation ** libs specified C++17 using C++ compiler: ‘clang version 21.1.8’ 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 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::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>::destroy' 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>::__on_zero_shared_impl, 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>::__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>::__shared_ptr_emplace &, const unsigned long &, unsigned long &, std::allocator, 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, std::shared_ptr &, 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 &, const unsigned long &, unsigned long &, 0>' requested here 542 | lambda[directed[i - 1]][i] = std::make_shared(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::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>::destroy' 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>::__on_zero_shared_impl, 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>::__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>::__shared_ptr_emplace &, unsigned long &, unsigned long &, std::allocator, 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, std::shared_ptr &, 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 &, unsigned long &, unsigned long &, 0>' requested here 545 | omega[u][v] = std::make_shared(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::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>::destroy' 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>::__on_zero_shared_impl, 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>::__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>::__shared_ptr_emplace, 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, 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' requested here 553 | sigma[i][j] = std::make_shared(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 -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 /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 -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)