* installing *source* package ‘spNetwork’ ... ** package ‘spNetwork’ 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)’ using C++17 make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/spNetwork/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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c base_kernel_funtions.cpp -o base_kernel_funtions.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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c border_correction.cpp -o border_correction.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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c bw_selection_nkde.cpp -o bw_selection_nkde.o bw_selection_nkde.cpp:37:7: warning: unused variable 'depth' [-Wunused-variable] 37 | int depth = 0; | ^~~~~ bw_selection_nkde.cpp:145:7: warning: unused variable 'depth' [-Wunused-variable] 145 | int depth = 0; | ^~~~~ bw_selection_nkde.cpp:267:7: warning: unused variable 'depth' [-Wunused-variable] 267 | int depth = 0; | ^~~~~ /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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c bw_selection_tnkde.cpp -o bw_selection_tnkde.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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c geometrical_functions.cpp -o geometrical_functions.o 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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c k_and_g_func.cpp -o k_and_g_func.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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c matrices_functions.cpp -o matrices_functions.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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c nkde_continuous.cpp -o nkde_continuous.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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c nkde_discontinuous.cpp -o nkde_discontinuous.o bw_selection_tnkde.cpp:41:7: warning: unused variable 'depth' [-Wunused-variable] 41 | int depth = 0; | ^~~~~ bw_selection_tnkde.cpp:172:8: warning: unused variable 'depth' [-Wunused-variable] 172 | int depth = 0; | ^~~~~ bw_selection_tnkde.cpp:188:11: warning: unused variable 'bw_net' [-Wunused-variable] 188 | double bw_net, bw_time; | ^~~~~~ bw_selection_tnkde.cpp:188:19: warning: unused variable 'bw_time' [-Wunused-variable] 188 | double bw_net, bw_time; | ^~~~~~~ bw_selection_tnkde.cpp:325:7: warning: unused variable 'depth' [-Wunused-variable] 325 | int depth = 0; | ^~~~~ bw_selection_tnkde.cpp:475:8: warning: unused variable 'depth' [-Wunused-variable] 475 | int depth = 0; | ^~~~~ bw_selection_tnkde.cpp:489:11: warning: unused variable 'bw_net' [-Wunused-variable] 489 | double bw_net, bw_time; | ^~~~~~ bw_selection_tnkde.cpp:489:19: warning: unused variable 'bw_time' [-Wunused-variable] 489 | double bw_net, bw_time; | ^~~~~~~ bw_selection_tnkde.cpp:643:7: warning: unused variable 'depth' [-Wunused-variable] 643 | int depth = 0; | ^~~~~ bw_selection_tnkde.cpp:846:8: warning: unused variable 'depth' [-Wunused-variable] 846 | int depth = 0; | ^~~~~ bw_selection_tnkde.cpp:856:8: warning: unused variable 'n_bw_net' [-Wunused-variable] 856 | int n_bw_net = bws_net.n_rows; | ^~~~~~~~ bw_selection_tnkde.cpp:857:8: warning: unused variable 'n_bw_time' [-Wunused-variable] 857 | int n_bw_time = bws_time.n_cols; | ^~~~~~~~~ bw_selection_tnkde.cpp:866:19: warning: unused variable 'bw_time' [-Wunused-variable] 866 | double bw_net, bw_time; | ^~~~~~~ bw_selection_tnkde.cpp:997:8: warning: unused variable 'n_net' [-Wunused-variable] 997 | int n_net = bws_net.n_rows; | ^~~~~ /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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c spatial_indexing.cpp -o spatial_indexing.o k_and_g_func.cpp:295:13: warning: unused variable 'dtime' [-Wunused-variable] 295 | float dtime = breaks_time[j]; | ^~~~~ /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/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -c spatial_indexing_export.cpp -o spatial_indexing_export.o 1 warning generated. 14 warnings generated. geometrical_functions.cpp:260:22: warning: unused variable 'x3' [-Wunused-variable] 260 | double x2,y2,x1,y1,x3,y3,dd; | ^~ geometrical_functions.cpp:260:25: warning: unused variable 'y3' [-Wunused-variable] 260 | double x2,y2,x1,y1,x3,y3,dd; | ^~ geometrical_functions.cpp:324:13: warning: unused variable 'dd' [-Wunused-variable] 324 | double d, dd, totald, dt, t; | ^~ geometrical_functions.cpp:324:17: warning: unused variable 'totald' [-Wunused-variable] 324 | double d, dd, totald, dt, t; | ^~~~~~ geometrical_functions.cpp:324:25: warning: unused variable 'dt' [-Wunused-variable] 324 | double d, dd, totald, dt, t; | ^~ geometrical_functions.cpp:324:29: warning: unused variable 't' [-Wunused-variable] 324 | double d, dd, totald, dt, t; | ^ geometrical_functions.cpp:326:7: warning: unused variable 'j' [-Wunused-variable] 326 | int j; | ^ geometrical_functions.cpp:327:10: warning: unused variable 'x2' [-Wunused-variable] 327 | double x2,y2,x1,y1,x3,y3; | ^~ geometrical_functions.cpp:327:13: warning: unused variable 'y2' [-Wunused-variable] 327 | double x2,y2,x1,y1,x3,y3; | ^~ geometrical_functions.cpp:327:16: warning: unused variable 'x1' [-Wunused-variable] 327 | double x2,y2,x1,y1,x3,y3; | ^~ geometrical_functions.cpp:327:19: warning: unused variable 'y1' [-Wunused-variable] 327 | double x2,y2,x1,y1,x3,y3; | ^~ geometrical_functions.cpp:327:22: warning: unused variable 'x3' [-Wunused-variable] 327 | double x2,y2,x1,y1,x3,y3; | ^~ geometrical_functions.cpp:327:25: warning: unused variable 'y3' [-Wunused-variable] 327 | double x2,y2,x1,y1,x3,y3; | ^~ geometrical_functions.cpp:440:31: warning: unused variable 'diff' [-Wunused-variable] 440 | float start_dist, end_dist, diff, line_length; | ^~~~ geometrical_functions.cpp:440:37: warning: unused variable 'line_length' [-Wunused-variable] 440 | float start_dist, end_dist, diff, line_length; | ^~~~~~~~~~~ geometrical_functions.cpp:973:9: warning: unused variable 'j' [-Wunused-variable] 973 | int i,j; | ^ geometrical_functions.cpp:1040:9: warning: unused variable 'j' [-Wunused-variable] 1040 | int i,j; | ^ In file included from geometrical_functions.cpp:5: In file included from ./spNetwork.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, 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:522:12: note: in instantiation of function template specialization 'arma::Mat::operator=, arma::op_sort_index>' requested here 522 | Mat::operator=(X.get_ref()); | ^ geometrical_functions.cpp:679:20: note: in instantiation of function template specialization 'arma::Col::Col, arma::op_sort_index>>' requested here 679 | uvec order = sort_index(total_mat.col(2)); | ^ /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__]] | ^ 18 warnings 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 spNetwork.so RcppExports.o base_kernel_funtions.o border_correction.o bw_selection_nkde.o bw_selection_tnkde.o geometrical_functions.o k_and_g_func.o matrices_functions.o nkde_continuous.o nkde_discontinuous.o spatial_indexing.o spatial_indexing_export.o make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/spNetwork/src' make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/spNetwork/src' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/spNetwork/src' installing to /data/gannet/ripley/R/packages/tests-Intel/spNetwork.Rcheck/00LOCK-spNetwork/00new/spNetwork/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (spNetwork)