* installing *source* package ‘bnclassify’ ...
** package ‘bnclassify’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/bnclassify/src'
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c anb-operate.cpp -o anb-operate.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c basic-misc.cpp -o basic-misc.o
basic-misc.cpp:29:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if (x.isNotNull() & y.isNotNull()) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
basic-misc.cpp:29:7: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c basic-probs.cpp -o basic-probs.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c bh.cpp -o bh.o
In file included from bh.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
property_ptr m_property;
^
bh.cpp:142:16: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_weight_t, double>>' requested here
ugraph g = r2graph<ugraph>(vertices, edges);
^
/usr/local/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/usr/local/bin/../include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/local/bin/../include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
bh.cpp:70:12: warning: unused variable 'index' [-Wunused-variable]
IndexMap index = get(vertex_index, original_graph);
^
bh.cpp:198:10: note: in instantiation of function template specialization 'graph2R<boost::filtered_graph<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_index_t, int, boost::property<boost::edge_weight_t, double>>>, boost::keep_all, remove_names<boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_index_t, int, boost::property<boost::edge_weight_t, double>>>, boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_index_t, int, boost::property<boost::edge_weight_t, double>>> *, std::string, std::string &, boost::vertex_name_t>>>, boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_index_t, int, boost::property<boost::edge_weight_t, double>>>>' requested here
return graph2R(fg, g);
^
bh.cpp:70:12: warning: unused variable 'index' [-Wunused-variable]
IndexMap index = get(vertex_index, original_graph);
^
bh.cpp:216:10: note: in instantiation of function template specialization 'graph2R<boost::filtered_graph<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_weight_t, double>>, remove_edge_names<boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_weight_t, double>>, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_weight_t, double>> *, std::string, std::string &, boost::vertex_name_t>, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_weight_t, double>>>>, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_weight_t, double>>>' requested here
return graph2R(fg, g);
^
bh.cpp:70:12: warning: unused variable 'index' [-Wunused-variable]
IndexMap index = get(vertex_index, original_graph);
^
bh.cpp:272:10: note: in instantiation of function template specialization 'graph2R<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_weight_t, double>>, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_name_t, std::string>>, boost::property<boost::edge_weight_t, double>>>' requested here
return graph2R(krusk, krusk);
^
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c data.cpp -o data.o
4 warnings generated.
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c graph-internal.cpp -o graph-internal.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c infer-test-wrappers.cpp -o infer-test-wrappers.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c infer.cpp -o infer.o
In file included from infer.cpp:1:
../inst/include/infer.h:114:15: warning: private field 'cpt' is not used [-Wunused-private-field]
const CPT & cpt;
^
1 warning generated.
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c multidim-array.cpp -o multidim-array.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang/include -DNO_S_TYPEDEFS -fpic -g -O3 -Wall -pedantic -frtti -c table.cpp -o table.o
clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o bnclassify.so RcppExports.o anb-operate.o basic-misc.o basic-probs.o bh.o data.o graph-internal.o infer-test-wrappers.o infer.o multidim-array.o table.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/bnclassify/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/bnclassify/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/bnclassify/src'
installing to /data/gannet/ripley/R/packages/tests-clang/bnclassify.Rcheck/00LOCK-bnclassify/00new/bnclassify/libs
** R
** data
** 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 (bnclassify)