* installing *source* package ‘CaseBasedReasoning’ ... ** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602)’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning/src' /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c RcppExports.cpp -o RcppExports.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c distanceAPI.cpp -o distanceAPI.o In file included from distanceAPI.cpp:1: In file included from ./distanceAPI.h:7: ./distance/distance.h:60:17: warning: variable 'nTree' set but not used [-Wunused-but-set-variable] 60 | std::size_t nTree = 0; | ^ distanceAPI.cpp:46:7: warning: unused variable 'ncols' [-Wunused-variable] 46 | int ncols = y.n_rows; | ^~~~~ In file included from distanceAPI.cpp:1: In file included from ./distanceAPI.h:5: In file included from /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25: In file included from /data/gannet2/ripley/R/test-MKL/Rcpp/include/RcppCommon.h:30: In file included from /data/gannet2/ripley/R/test-MKL/Rcpp/include/Rcpp/r/headers.h:62: In file included from /data/gannet2/ripley/R/test-MKL/Rcpp/include/Rcpp/platform/compiler.h:153: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/unordered_map:41: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/ext/alloc_traits.h:34: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/alloc_traits.h:33: /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_construct.h:151:7: warning: destructor called on non-final 'rangerProximity' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] 151 | __pointer->~_Tp(); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/alloc_traits.h:648:9: note: in instantiation of function template specialization 'std::_Destroy' requested here 648 | { std::_Destroy(__p); } | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/shared_ptr_base.h:613:28: note: in instantiation of function template specialization 'std::allocator_traits>::destroy' requested here 613 | allocator_traits<_Alloc>::destroy(_M_impl._M_alloc(), _M_ptr()); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/shared_ptr_base.h:599:2: note: in instantiation of member function 'std::_Sp_counted_ptr_inplace, __gnu_cxx::_S_atomic>::_M_dispose' requested here 599 | _Sp_counted_ptr_inplace(_Alloc __a, _Args&&... __args) | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/shared_ptr_base.h:972:6: note: in instantiation of function template specialization 'std::_Sp_counted_ptr_inplace, __gnu_cxx::_S_atomic>::_Sp_counted_ptr_inplace' requested here 972 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/shared_ptr_base.h:1712:14: note: in instantiation of function template specialization 'std::__shared_count<>::__shared_count, rangerProximity &>' requested here 1712 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/shared_ptr.h:464:4: note: in instantiation of function template specialization 'std::__shared_ptr::__shared_ptr, rangerProximity &>' requested here 464 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/shared_ptr.h:1009:14: note: in instantiation of function template specialization 'std::shared_ptr::shared_ptr, rangerProximity &>' requested here 1009 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^ distanceAPI.cpp:73:16: note: in instantiation of function template specialization 'std::make_shared' requested here 73 | dist_ = std::make_shared(dist); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_construct.h:151:19: note: qualify call to silence this warning 151 | __pointer->~_Tp(); | ^ 3 warnings generated. /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c distances.cpp -o distances.o In file included from distances.cpp:4: In file included from ./distanceAPI.h:7: ./distance/distance.h:60:17: warning: variable 'nTree' set but not used [-Wunused-but-set-variable] 60 | std::size_t nTree = 0; | ^ 1 warning generated. /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c order.cpp -o order.o In file included from order.cpp:3: In file included from /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25: In file included from /data/gannet2/ripley/R/test-MKL/Rcpp/include/RcppCommon.h:62: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/functional:64: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:61: /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:263:8: warning: 'get_temporary_buffer>' is deprecated [-Wdeprecated-declarations] 263 | std::get_temporary_buffer(_M_original_len)); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:4996:15: note: in instantiation of member function 'std::_Temporary_buffer<__gnu_cxx::__normal_iterator *, std::vector>>, arma::arma_sort_index_packet>::_Temporary_buffer' requested here 4996 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:5070:23: note: in instantiation of function template specialization 'std::__stable_sort<__gnu_cxx::__normal_iterator *, std::vector>>, __gnu_cxx::__ops::_Iter_comp_iter>>' requested here 5070 | _GLIBCXX_STD_A::__stable_sort(__first, __last, | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_sort_index_meat.hpp:85:12: note: in instantiation of function template specialization 'std::stable_sort<__gnu_cxx::__normal_iterator *, std::vector>>, arma::arma_sort_index_helper_ascend>' requested here 85 | std::stable_sort( packet_vec.begin(), packet_vec.end(), comparator ); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_sort_index_meat.hpp:123:10: note: in instantiation of function template specialization 'arma::arma_sort_index_helper, false>' requested here 123 | return arma_sort_index_helper(out, P, sort_type); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_sort_index_meat.hpp:147:34: note: in instantiation of function template specialization 'arma::op_sort_index::apply_noalias>' requested here 147 | all_non_nan = op_sort_index::apply_noalias(out2, P, sort_type); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:5234:12: note: in instantiation of function template specialization 'arma::op_sort_index::apply>' requested here 5234 | op_type::apply(*this, X); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Col_meat.hpp:535:12: note: in instantiation of function template specialization 'arma::Mat::operator=, arma::op_sort_index>' requested here 535 | Mat::operator=(X.get_ref()); | ^ order.cpp:26:13: note: in instantiation of function template specialization 'arma::Col::operator=, arma::op_sort_index>>' requested here 26 | order = arma::sort_index(x_.col(i), "ascend"); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:99:5: note: 'get_temporary_buffer>' has been explicitly marked deprecated here 99 | _GLIBCXX17_DEPRECATED | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2359:34: note: expanded from macro '_GLIBCXX17_DEPRECATED' 2359 | # define _GLIBCXX17_DEPRECATED [[__deprecated__]] | ^ 1 warning generated. /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c weightedKNN.cpp -o weightedKNN.o In file included from weightedKNN.cpp:2: In file included from /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25: In file included from /data/gannet2/ripley/R/test-MKL/Rcpp/include/RcppCommon.h:62: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/functional:64: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:61: /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:263:8: warning: 'get_temporary_buffer>' is deprecated [-Wdeprecated-declarations] 263 | std::get_temporary_buffer(_M_original_len)); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:4996:15: note: in instantiation of member function 'std::_Temporary_buffer<__gnu_cxx::__normal_iterator *, std::vector>>, arma::arma_sort_index_packet>::_Temporary_buffer' requested here 4996 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:5070:23: note: in instantiation of function template specialization 'std::__stable_sort<__gnu_cxx::__normal_iterator *, std::vector>>, __gnu_cxx::__ops::_Iter_comp_iter>>' requested here 5070 | _GLIBCXX_STD_A::__stable_sort(__first, __last, | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_sort_index_meat.hpp:85:12: note: in instantiation of function template specialization 'std::stable_sort<__gnu_cxx::__normal_iterator *, std::vector>>, arma::arma_sort_index_helper_ascend>' requested here 85 | std::stable_sort( packet_vec.begin(), packet_vec.end(), comparator ); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_sort_index_meat.hpp:123:10: note: in instantiation of function template specialization 'arma::arma_sort_index_helper, false>' requested here 123 | return arma_sort_index_helper(out, P, sort_type); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_sort_index_meat.hpp:147:34: note: in instantiation of function template specialization 'arma::op_sort_index::apply_noalias>' requested here 147 | all_non_nan = op_sort_index::apply_noalias(out2, P, sort_type); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:5234:12: note: in instantiation of function template specialization 'arma::op_sort_index::apply>' requested here 5234 | op_type::apply(*this, X); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Col_meat.hpp:535:12: note: in instantiation of function template specialization 'arma::Mat::operator=, arma::op_sort_index>' requested here 535 | Mat::operator=(X.get_ref()); | ^ weightedKNN.cpp:27:11: note: in instantiation of function template specialization 'arma::Col::operator=, arma::op_sort_index>>' requested here 27 | order = arma::sort_index(tmpDist, "ascend"); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:99:5: note: 'get_temporary_buffer>' has been explicitly marked deprecated here 99 | _GLIBCXX17_DEPRECATED | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2359:34: note: expanded from macro '_GLIBCXX17_DEPRECATED' 2359 | # define _GLIBCXX17_DEPRECATED [[__deprecated__]] | ^ 1 warning generated. /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -shared -L/data/gannet/ripley/intel/oneapi/compiler/2024.1/lib -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o order.o weightedKNN.o make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning/src' make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning/src' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning/src' installing to /data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning.Rcheck/00LOCK-CaseBasedReasoning/00new/CaseBasedReasoning/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CaseBasedReasoning)