* installing *source* package ‘FRESA.CAD’ ...
** package ‘FRESA.CAD’ 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/FRESA.CAD/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   -fiopenmp -fpic  -O3 -fp-model precise -Wall   -c FRESACAD_init.cpp -o FRESACAD_init.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   -fiopenmp -fpic  -O3 -fp-model precise -Wall   -c FRESAcommons.cpp -o FRESAcommons.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   -fiopenmp -fpic  -O3 -fp-model precise -Wall   -c binaryFeatureSelectionCpp.cpp -o binaryFeatureSelectionCpp.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   -fiopenmp -fpic  -O3 -fp-model precise -Wall   -c rankInverseNormalCpp.cpp -o rankInverseNormalCpp.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   -fiopenmp -fpic  -O3 -fp-model precise -Wall   -c regresionFeatureSelectionCpp.cpp -o regresionFeatureSelectionCpp.o
FRESAcommons.cpp:441:13: warning: variable 'nrisk' set but not used [-Wunused-but-set-variable]
  441 |     int     nrisk;    
      |             ^
In file included from binaryFeatureSelectionCpp.cpp:20:
In file included from ./FRESAcommons.h:24:
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<arma::arma_sort_index_packet<double>>' is deprecated [-Wdeprecated-declarations]
  263 |                 std::get_temporary_buffer<value_type>(_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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, arma::arma_sort_index_packet<double>>::_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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_ascend<double>>>' 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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, arma::arma_sort_index_helper_ascend<double>>' 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::Mat<double>, false>' requested here
  123 |   return arma_sort_index_helper<T1,false>(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::Mat<double>>' 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:5221:12: note: in instantiation of function template specialization 'arma::op_sort_index::apply<arma::Mat<double>>' requested here
 5221 |   op_type::apply(*this, X);
      |            ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Proxy.hpp:666:7: note: in instantiation of function template specialization 'arma::Mat<unsigned int>::Mat<arma::Mat<double>, arma::op_sort_index>' requested here
  666 |     : Q(A)
      |       ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/eGlue_meat.hpp:36:5: note: in instantiation of member function 'arma::Proxy<arma::mtOp<unsigned int, arma::Mat<double>, arma::op_sort_index>>::Proxy' requested here
   36 |   : P1(in_A)
      |     ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/operator_plus.hpp:127:10: note: in instantiation of member function 'arma::eGlue<arma::mtOp<unsigned int, arma::Mat<double>, arma::op_sort_index>, arma::Gen<arma::Col<unsigned int>, arma::gen_ones>, arma::eglue_plus>::eGlue' requested here
  127 |   return eGlue<T1, T2, eglue_plus>(X, Y);
      |          ^
binaryFeatureSelectionCpp.cpp:425:58: note: in instantiation of function template specialization 'arma::operator+<arma::mtOp<unsigned int, arma::Mat<double>, arma::op_sort_index>, arma::Gen<arma::Col<unsigned int>, arma::gen_ones>>' requested here
  425 |                                         rindex = sort_index(randu<vec>(casesample.n_cols-1))+ones<uvec>(casesample.n_cols-1);
      |                                                                                             ^
/usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:99:5: note: 'get_temporary_buffer<arma::arma_sort_index_packet<double>>' 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 regresionFeatureSelectionCpp.cpp:19:
In file included from ./FRESAcommons.h:24:
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<arma::arma_sort_index_packet<double>>' is deprecated [-Wdeprecated-declarations]
  263 |                 std::get_temporary_buffer<value_type>(_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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, arma::arma_sort_index_packet<double>>::_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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_ascend<double>>>' 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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, arma::arma_sort_index_helper_ascend<double>>' 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::Mat<double>, false>' requested here
  123 |   return arma_sort_index_helper<T1,false>(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::Mat<double>>' 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:5221:12: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
 5221 |   op_type::apply(*this, X);
      |            ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/unwrap.hpp:1056:7: note: in instantiation of function template specialization 'arma::Mat<unsigned int>::Mat<arma::Mat<double>, arma::op_sort_index>' requested here
 1056 |     : M(A)
      |       ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/subview_elem1_meat.hpp:788:32: note: in instantiation of function template specialization 'arma::unwrap_check_mixed<arma::mtOp<unsigned int, arma::Mat<double>, arma::op_sort_index>>::unwrap_check_mixed<double>' requested here
  788 |   const unwrap_check_mixed<T1> tmp1(in.a.get_ref(), actual_out);
      |                                ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2441:25: note: in instantiation of member function 'arma::subview_elem1<double, arma::mtOp<unsigned int, arma::Mat<double>, arma::op_sort_index>>::extract' requested here
 2441 |   subview_elem1<eT,T1>::extract(*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<double>::operator=<arma::mtOp<unsigned int, arma::Mat<double>, arma::op_sort_index>>' requested here
  535 |   Mat<eT>::operator=(X.get_ref());
      |            ^
regresionFeatureSelectionCpp.cpp:303:14: note: in instantiation of function template specialization 'arma::Col<double>::operator=<arma::subview_elem1<double, arma::mtOp<unsigned int, arma::Mat<double>, arma::op_sort_index>>>' requested here
  303 |                 randOutput =  randOutput(sort_index(randu<vec>(dataframe.n_rows)));
      |                            ^
/usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:99:5: note: 'get_temporary_buffer<arma::arma_sort_index_packet<double>>' 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 FRESAcommons.cpp:20:
In file included from ./FRESAcommons.h:24:
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<arma::arma_sort_index_packet<double>>' is deprecated [-Wdeprecated-declarations]
  263 |                 std::get_temporary_buffer<value_type>(_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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, arma::arma_sort_index_packet<double>>::_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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_ascend<double>>>' 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<arma::arma_sort_index_packet<double> *, std::vector<arma::arma_sort_index_packet<double>>>, arma::arma_sort_index_helper_ascend<double>>' 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::Mat<double>, false>' requested here
  123 |   return arma_sort_index_helper<T1,false>(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::Mat<double>>' 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::Mat<double>>' 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<unsigned int>::operator=<arma::Mat<double>, arma::op_sort_index>' requested here
  522 |   Mat<eT>::operator=(X.get_ref());
      |            ^
FRESAcommons.cpp:152:15: note: in instantiation of function template specialization 'arma::Col<unsigned int>::Col<arma::mtOp<unsigned int, arma::Mat<double>, arma::op_sort_index>>' requested here
  152 |         uvec uidex = sort_index(times); 
      |                      ^
/usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:99:5: note: 'get_temporary_buffer<arma::arma_sort_index_packet<double>>' 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.
2 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 FRESA.CAD.so FRESACAD_init.o FRESAcommons.o binaryFeatureSelectionCpp.o rankInverseNormalCpp.o regresionFeatureSelectionCpp.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 -fiopenmp
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/FRESA.CAD/src'
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/FRESA.CAD/src'
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/FRESA.CAD/src'
installing to /data/gannet/ripley/R/packages/tests-Intel/FRESA.CAD.Rcheck/00LOCK-FRESA.CAD/00new/FRESA.CAD/libs
** R
** data
** inst
** 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 (FRESA.CAD)