* installing *source* package ‘pcalg’ ... ** package ‘pcalg’ 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++ 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/pcalg/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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -I"../inst/include" -fpic -O3 -fp-model precise -Wall -c constraint.cpp -o constraint.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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -I"../inst/include" -fpic -O3 -fp-model precise -Wall -c gies.cpp -o gies.o In file included from constraint.cpp:8: In file included from ../inst/include/pcalg/constraint.hpp:8: ../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 17 | #define NDEBUG | ^ :1:9: note: previous definition is here 1 | #define NDEBUG 1 | ^ In file included from constraint.cpp:8: In file included from ../inst/include/pcalg/constraint.hpp:10: In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/scoped_ptr.hpp:13: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here 408 | property_ptr m_property; | ^ /data/gannet/ripley/R/test-dev/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ../inst/include/pcalg/constraint.hpp:14:16: note: in instantiation of template class 'boost::graph_traits>' requested here 14 | typedef boost::graph_traits::out_edge_iterator UndirOutEdgeIter; | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here 287 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2344:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 2344 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2336:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 2336 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ In file included from gies.cpp:21: In file included from ../inst/include/pcalg/constraint.hpp:8: ../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 17 | #define NDEBUG | ^ :1:9: note: previous definition is here 1 | #define NDEBUG 1 | ^ In file included from gies.cpp:12: In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/scoped_ptr.hpp:13: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here 408 | property_ptr m_property; | ^ /data/gannet/ripley/R/test-dev/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ../inst/include/pcalg/constraint.hpp:14:16: note: in instantiation of template class 'boost::graph_traits>' requested here 14 | typedef boost::graph_traits::out_edge_iterator UndirOutEdgeIter; | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here 287 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2344:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 2344 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2336:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 2336 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ In file included from constraint.cpp:8: In file included from ../inst/include/pcalg/constraint.hpp:8: In file included from ../inst/include/pcalg/armaLapack.hpp:15: 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 1 context 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/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()); | ^ /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_pinv_meat.hpp:137:21: note: in instantiation of function template specialization 'arma::op_pinv::apply_sym' requested here 137 | return op_pinv::apply_sym(out, A, tol, method_id); | ^ /data/gannet2/ripley/R/test-MKL/RcppArmadillo/include/armadillo_bits/fn_pinv.hpp:97:32: note: in instantiation of function template specialization 'arma::op_pinv::apply_direct>' requested here 97 | const bool status = op_pinv::apply_direct(out, X.get_ref(), tol, method_id); | ^ constraint.cpp:58:3: note: in instantiation of function template specialization 'arma::pinv>' requested here 58 | pinv(PM, C_sub); | ^ /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__]] | ^ 2 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/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -I"../inst/include" -fpic -O3 -fp-model precise -Wall -c greedy.cpp -o greedy.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icx -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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -O3 -fp-model precise -Wall -Wstrict-prototypes -c init.c -o init.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/gannet2/ripley/R/test-MKL/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -I"../inst/include" -fpic -O3 -fp-model precise -Wall -c score.cpp -o score.o In file included from greedy.cpp:8: In file included from ../inst/include/pcalg/greedy.hpp:11: In file included from ../inst/include/pcalg/score.hpp:12: ../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 17 | #define NDEBUG | ^ :1:9: note: previous definition is here 1 | #define NDEBUG 1 | ^ In file included from greedy.cpp:8: In file included from ../inst/include/pcalg/greedy.hpp:18: In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/scoped_ptr.hpp:13: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here 408 | property_ptr m_property; | ^ /data/gannet/ripley/R/test-dev/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ../inst/include/pcalg/greedy.hpp:57:16: note: in instantiation of template class 'boost::graph_traits>' requested here 57 | typedef boost::graph_traits::vertex_descriptor vertex_t; | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here 287 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2344:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 2344 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2336:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 2336 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ greedy.cpp:862:30: warning: unused variable 'vi' [-Wunused-variable] 862 | std::vector::iterator vi; | ^~ In file included from score.cpp:6: In file included from ../inst/include/pcalg/score.hpp:12: ../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 17 | #define NDEBUG | ^ :1:9: note: previous definition is here 1 | #define NDEBUG 1 | ^ In file included from score.cpp:7: In file included from ../inst/include/pcalg/greedy.hpp:18: In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/scoped_ptr.hpp:13: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here 408 | property_ptr m_property; | ^ /data/gannet/ripley/R/test-dev/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ../inst/include/pcalg/greedy.hpp:57:16: note: in instantiation of template class 'boost::graph_traits>' requested here 57 | typedef boost::graph_traits::vertex_descriptor vertex_t; | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here 287 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2344:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 2344 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2336:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 2336 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ score.cpp:170:29: warning: unused variable 'vi' [-Wunused-variable] 170 | std::vector::iterator vi; | ^~ 3 warnings generated. 3 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 pcalg.so constraint.o gies.o greedy.o init.o score.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/pcalg/src' make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/pcalg/src' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/pcalg/src' installing to /data/gannet/ripley/R/packages/tests-Intel/pcalg.Rcheck/00LOCK-pcalg/00new/pcalg/libs ** R ** data ** 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 (pcalg)