* installing *source* package ‘PAGFL’ ...
** package ‘PAGFL’ 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/PAGFL/src'
/data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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   -fiopenmp -fpic  -O3 -fp-model precise -Wall   -c PAGFL-package.cpp -o PAGFL-package.o
In file included from PAGFL-package.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<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::Col<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::Col<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: (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<double>' 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<arma::Op<arma::Mat<double>, arma::op_trimat>, false>' requested here
   49 |   return op_inv_gen_full::apply_direct<T1,false>(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<arma::Op<arma::Mat<double>, arma::op_trimat>>' 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<arma::Op<arma::Mat<double>, arma::op_trimat>>' requested here
 4945 |   op_type::apply(*this, X);
      |            ^
PAGFL-package.cpp:87:26: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Op<arma::Mat<double>, arma::op_trimat>, arma::op_inv_gen_default>' requested here
   87 |     arma::mat chol_inv = arma::inv(arma::trimatu(chol_decomp));
      |                          ^
/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 PAGFL-package.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<arma::arma_sort_index_packet<unsigned long long>>' 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<unsigned long long> *, std::vector<arma::arma_sort_index_packet<unsigned long long>>>, arma::arma_sort_index_packet<unsigned long long>>::_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<unsigned long long> *, std::vector<arma::arma_sort_index_packet<unsigned long long>>>, __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_ascend<unsigned long long>>>' 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<unsigned long long> *, std::vector<arma::arma_sort_index_packet<unsigned long long>>>, arma::arma_sort_index_helper_ascend<unsigned long long>>' 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:168:10: note: in instantiation of function template specialization 'arma::arma_sort_index_helper<arma::Mat<unsigned long long>, true>' requested here
  168 |   return arma_sort_index_helper<T1,true>(out, P, sort_type);
      |          ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/op_sort_index_meat.hpp:192:41: note: in instantiation of function template specialization 'arma::op_stable_sort_index::apply_noalias<arma::Mat<unsigned long long>>' requested here
  192 |     all_non_nan = op_stable_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/glue_intersect_meat.hpp:91:19: note: in instantiation of function template specialization 'arma::Col<unsigned long long>::operator=<arma::mtOp<unsigned long long, arma::Mat<unsigned long long>, arma::op_stable_sort_index>>' requested here
   91 |     C_sorted_indx = stable_sort_index(C);
      |                   ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/glue_intersect_meat.hpp:34:19: note: in instantiation of function template specialization 'arma::glue_intersect::apply<arma::Mat<unsigned long long>, arma::Mat<unsigned long long>>' requested here
   34 |   glue_intersect::apply(out, iA, iB, X.A, X.B, false);
      |                   ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:5603:14: note: in instantiation of function template specialization 'arma::glue_intersect::apply<arma::Col<unsigned long long>, arma::Col<unsigned long long>>' 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<unsigned long long>::operator=<arma::Col<unsigned long long>, arma::Col<unsigned long long>, arma::glue_intersect>' requested here
  522 |   Mat<eT>::operator=(X.get_ref());
      |            ^
PAGFL-package.cpp:976:40: note: in instantiation of function template specialization 'arma::Col<unsigned long long>::Col<arma::Glue<arma::Col<unsigned long long>, arma::Col<unsigned long long>, arma::glue_intersect>>' requested here
  976 |                 arma::uvec intersect = arma::intersect(groupList[i], groupList[j]);
      |                                        ^
/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<unsigned long long>>' 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__]]
      |                                  ^
/data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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   -fiopenmp -fpic  -O3 -fp-model precise -Wall   -c RcppExports.cpp -o RcppExports.o
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 PAGFL.so PAGFL-package.o RcppExports.o -fiopenmp -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/PAGFL/src'
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/PAGFL/src'
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/PAGFL/src'
installing to /data/gannet/ripley/R/packages/tests-Intel/PAGFL.Rcheck/00LOCK-PAGFL/00new/PAGFL/libs
** R
** 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 (PAGFL)