* installing *source* package ‘BGVAR’ ... ** package ‘BGVAR’ 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/BGVAR/src' /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I../inst/include/ -DARMA_NO_DEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I'/data/gannet2/ripley/R/test-MKL/stochvol/include' -I'/data/gannet2/ripley/R/test-MKL/GIGrvg/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c BVAR_linear.cpp -o BVAR_linear.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I../inst/include/ -DARMA_NO_DEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I'/data/gannet2/ripley/R/test-MKL/stochvol/include' -I'/data/gannet2/ripley/R/test-MKL/GIGrvg/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../inst/include/ -DARMA_NO_DEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I'/data/gannet2/ripley/R/test-MKL/stochvol/include' -I'/data/gannet2/ripley/R/test-MKL/GIGrvg/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c do_rgig1.cpp -o do_rgig1.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I../inst/include/ -DARMA_NO_DEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I'/data/gannet2/ripley/R/test-MKL/stochvol/include' -I'/data/gannet2/ripley/R/test-MKL/GIGrvg/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c gvar_stacking.cpp -o gvar_stacking.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I../inst/include/ -DARMA_NO_DEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I'/data/gannet2/ripley/R/test-MKL/stochvol/include' -I'/data/gannet2/ripley/R/test-MKL/GIGrvg/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c helper.cpp -o helper.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I../inst/include/ -DARMA_NO_DEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppParallel/include' -I'/data/gannet2/ripley/R/test-MKL/stochvol/include' -I'/data/gannet2/ripley/R/test-MKL/GIGrvg/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c irf.cpp -o irf.o In file included from BVAR_linear.cpp:1: 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 2 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/armadillo_bits/op_pinv_meat.hpp:211:24: note: in instantiation of function template specialization 'arma::Col::Col, arma::op_sort_index>>' requested here 211 | const uvec indices = sort_index(abs_eigval, "descend"); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_inv_spd_meat.hpp:141:23: note: in instantiation of function template specialization 'arma::op_pinv::apply_sym' requested here 141 | return op_pinv::apply_sym(out, A, T(0), uword(0)); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_inv_spd_meat.hpp:49:27: note: in instantiation of function template specialization 'arma::op_inv_spd_full::apply_direct, false>' requested here 49 | return op_inv_spd_full::apply_direct(out, expr, uword(0)); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/fn_inv_sympd.hpp:51:43: note: in instantiation of function template specialization 'arma::op_inv_spd_default::apply_direct>' requested here 51 | const bool status = op_inv_spd_default::apply_direct(out, X.get_ref()); | ^ /data/gannet2/ripley/R/test-MKL/stochvol/include/type_definitions.hpp:189:28: note: in instantiation of function template specialization 'arma::inv_sympd>' requested here 189 | bool success = arma::inv_sympd(precision, _covariance) and | ^ /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__]] | ^ In file included from gvar_stacking.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: (skipping 3 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/armadillo_bits/op_inv_gen_meat.hpp:140:48: note: in instantiation of function template specialization 'arma::op_pinv::apply_sym' requested here 140 | if(inv_state.is_sym ) { return op_pinv::apply_sym (out, A, T(0), uword(0)); } | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_inv_gen_meat.hpp:49:27: note: in instantiation of function template specialization 'arma::op_inv_gen_full::apply_direct, false>' requested here 49 | return op_inv_gen_full::apply_direct(out, expr, caller_sig, uword(0)); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_inv_gen_meat.hpp:31:43: note: in instantiation of function template specialization 'arma::op_inv_gen_default::apply_direct>' requested here 31 | const bool status = op_inv_gen_default::apply_direct(out, X.m, "inv()"); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:4945:12: note: in instantiation of function template specialization 'arma::op_inv_gen_default::apply>' requested here 4945 | op_type::apply(*this, X); | ^ gvar_stacking.cpp:113:16: note: in instantiation of function template specialization 'arma::Mat::Mat, arma::op_inv_gen_default>' requested here 113 | mat Ginv = G.i(); | ^ /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__]] | ^ In file included from helper.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: (skipping 10 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/armadillo_bits/glue_times_meat.hpp:411:69: note: in instantiation of function template specialization 'arma::glue_times_redirect3_helper::apply, arma::op_htrans>, arma::Mat, arma::glue_times>, arma::op_inv_gen_default>, arma::Op, arma::op_htrans>, arma::Mat>' requested here 411 | glue_times_redirect3_helper< is_supported_blas_type::value >::apply(out, X); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:488:31: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply, arma::op_htrans>, arma::Mat, arma::glue_times>, arma::op_inv_gen_default>, arma::Op, arma::op_htrans>, arma::Mat>' requested here 488 | glue_times_redirect::apply(out, X); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:5603:14: note: in instantiation of function template specialization 'arma::glue_times::apply, arma::op_htrans>, arma::Mat, arma::glue_times>, arma::op_inv_gen_default>, arma::Op, arma::op_htrans>, arma::glue_times>, arma::Mat>' requested here 5603 | glue_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::op_htrans>, arma::Mat, arma::glue_times>, arma::op_inv_gen_default>, arma::Op, arma::op_htrans>, arma::glue_times>, arma::Mat, arma::glue_times>' requested here 522 | Mat::operator=(X.get_ref()); | ^ helper.cpp:51:15: note: in instantiation of function template specialization 'arma::Col::Col, arma::op_htrans>, arma::Mat, arma::glue_times>, arma::op_inv_gen_default>, arma::Op, arma::op_htrans>, arma::glue_times>, arma::Mat, arma::glue_times>>' requested here 51 | vec b_OLS = inv(X.t() * X) * X.t() * Y; | ^ /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. 1 warning generated. 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 BGVAR.so BVAR_linear.o RcppExports.o do_rgig1.o gvar_stacking.o helper.o irf.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/BGVAR/src' make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/BGVAR/src' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/BGVAR/src' installing to /data/gannet/ripley/R/packages/tests-Intel/BGVAR.Rcheck/00LOCK-BGVAR/00new/BGVAR/libs ** R ** data *** moving datasets to lazyload DB ** 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 (BGVAR)