* installing *source* package ‘inferCSN’ ... ** package ‘inferCSN’ 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/inferCSN/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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c BetaVector.cpp -o BetaVector.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c CDL012LogisticSwaps.cpp -o CDL012LogisticSwaps.o In file included from CDL012LogisticSwaps.cpp:1: In file included from include/CDL012LogisticSwaps.h: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, arma::eop_abs>, 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, arma::eop_abs>>' 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, arma::eop_abs>>' requested here 5234 | op_type::apply(*this, X); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Col_meat.hpp:522:12: note: in instantiation of function template specialization 'arma::Mat::operator=, arma::eop_abs>, arma::op_sort_index>' requested here 522 | Mat::operator=(X.get_ref()); | ^ CDL012LogisticSwaps.cpp:68:34: note: in instantiation of function template specialization 'arma::Col::Col, arma::eop_abs>, arma::op_sort_index>>' requested here 68 | arma::uvec indices = arma::sort_index(arma::abs(gradient), "descend"); | ^ /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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c CDL012SquaredHingeSwaps.cpp -o CDL012SquaredHingeSwaps.o CDL012SquaredHingeSwaps.cpp:68:37: warning: variable 'l' set but not used [-Wunused-but-set-variable] 68 | std::size_t l = 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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c CDL012Swaps.cpp -o CDL012Swaps.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c Grid.cpp -o Grid.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c Grid1D.cpp -o Grid1D.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c Grid2D.cpp -o Grid2D.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c Interface.cpp -o Interface.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c Normalize.cpp -o Normalize.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c README.cpp -o README.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: 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: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 5234 | op_type::apply(*this, X); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloAs.h:113:38: note: in instantiation of function template specialization 'arma::SpMat::SpMat, arma::Row, arma::glue_join_cols>, arma::eop_scalar_minus_post>, arma::Mat>' requested here 113 | arma::SpMat res = arma::sp_mat(true, arma::join_cols(ti, tj)-1, tx, li["nrow"], li["ncol"], true, false); | ^ /data/gannet2/ripley/R/test-MKL/Rcpp/include/Rcpp/as.h:89:29: note: in instantiation of member function 'Rcpp::traits::Exporter>::get' requested here 89 | return exporter.get(); | ^ /data/gannet2/ripley/R/test-MKL/Rcpp/include/Rcpp/as.h:152:26: note: in instantiation of function template specialization 'Rcpp::internal::as>' requested here 152 | return internal::as(x, typename traits::r_type_traits::r_category()); | ^ /data/gannet2/ripley/R/test-MKL/Rcpp/include/Rcpp/InputParameter.h:72:54: note: in instantiation of function template specialization 'Rcpp::as>' requested here 72 | ConstReferenceInputParameter(SEXP x_) : obj( as(x_) ){} | ^ RcppExports.cpp:20:64: note: in instantiation of member function 'Rcpp::ConstReferenceInputParameter>::ConstReferenceInputParameter' requested here 20 | Rcpp::traits::input_parameter< const arma::sp_mat& >::type X(XSEXP); | ^ /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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c Test_Interface.cpp -o Test_Interface.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c asMatrix.cpp -o asMatrix.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c table_to_matrix.cpp -o table_to_matrix.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/usr/local/include "-Iinclude" -fpic -O3 -fp-model precise -Wall -c utils.cpp -o utils.o /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 inferCSN.so BetaVector.o CDL012LogisticSwaps.o CDL012SquaredHingeSwaps.o CDL012Swaps.o Grid.o Grid1D.o Grid2D.o Interface.o Normalize.o README.o RcppExports.o Test_Interface.o asMatrix.o table_to_matrix.o utils.o -L/data/gannet/ripley/intel/oneapi/mkl/2023.2.0/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/inferCSN/src' make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/inferCSN/src' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/inferCSN/src' installing to /data/gannet/ripley/R/packages/tests-Intel/inferCSN.Rcheck/00LOCK-inferCSN/00new/inferCSN/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (inferCSN)