* installing *source* package ‘CMGFM’ ...
** package ‘CMGFM’ 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/CMGFM/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 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/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I/usr/local/include   -fiopenmp  -fpic  -O3 -fp-model precise -Wall   -c cmgfm.cpp -o cmgfm.o
cmgfm.cpp:143:15: warning: unused variable 'qs1' [-Wunused-variable]
  143 |   int id, im, qs1,  d = Bf.n_cols, m=Bf.n_rows;
      |               ^~~
In file included from cmgfm.cpp:7:
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 12 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/Mat_meat.hpp:5586:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::op_inv_gen_default>, arma::Op<arma::Mat<double>, arma::op_htrans>, arma::glue_times>, arma::Op<arma::eGlue<arma::Mat<double>, arma::Op<arma::Op<arma::Col<double>, arma::op_htrans>, arma::op_repmat>, arma::eglue_schur>, arma::op_sum>>' requested here
 5586 |   glue_type::apply(*this, X);
      |              ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/Proxy.hpp:503:7: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::op_inv_gen_default>, arma::Op<arma::Mat<double>, arma::op_htrans>, arma::glue_times>, arma::Op<arma::eGlue<arma::Mat<double>, arma::Op<arma::Op<arma::Col<double>, arma::op_htrans>, arma::op_repmat>, arma::eglue_schur>, arma::op_sum>, arma::glue_times>' requested here
  503 |     : Q(A)
      |       ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/eOp_meat.hpp:37:5: note: in instantiation of member function 'arma::Proxy<arma::Glue<arma::Glue<arma::Op<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::op_inv_gen_default>, arma::Op<arma::Mat<double>, arma::op_htrans>, arma::glue_times>, arma::Op<arma::eGlue<arma::Mat<double>, arma::Op<arma::Op<arma::Col<double>, arma::op_htrans>, arma::op_repmat>, arma::eglue_schur>, arma::op_sum>, arma::glue_times>>::Proxy' requested here
   37 |   : P(in_m)
      |     ^
/data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/operator_div.hpp:37:10: note: in instantiation of member function 'arma::eOp<arma::Glue<arma::Glue<arma::Op<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::op_inv_gen_default>, arma::Op<arma::Mat<double>, arma::op_htrans>, arma::glue_times>, arma::Op<arma::eGlue<arma::Mat<double>, arma::Op<arma::Op<arma::Col<double>, arma::op_htrans>, arma::op_repmat>, arma::eglue_schur>, arma::op_sum>, arma::glue_times>, arma::eop_scalar_div_post>::eOp' requested here
   37 |   return eOp<T1, eop_scalar_div_post>(X, k);
      |          ^
cmgfm.cpp:66:96: note: in instantiation of function template specialization 'arma::operator/<arma::Glue<arma::Glue<arma::Op<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::op_inv_gen_default>, arma::Op<arma::Mat<double>, arma::op_htrans>, arma::glue_times>, arma::Op<arma::eGlue<arma::Mat<double>, arma::Op<arma::Op<arma::Col<double>, arma::op_htrans>, arma::op_repmat>, arma::eglue_schur>, arma::op_sum>, arma::glue_times>>' requested here
   66 |         vec_tmp = (Z.t()*Z).i() * Z.t() * sum(mat_tmp % repmat(invLambdaf(im, id).t(),n,1), 1) / accu(invLambdaf(im, id));
      |                                                                                                ^
/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__]]
      |                                  ^
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 CMGFM.so RcppExports.o cmgfm.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/CMGFM/src'
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/CMGFM/src'
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/CMGFM/src'
installing to /data/gannet/ripley/R/packages/tests-Intel/CMGFM.Rcheck/00LOCK-CMGFM/00new/CMGFM/libs
** R
** 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 (CMGFM)