##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RBGL.buildbin-libdir RBGL_1.60.0.tar.gz
###
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install for i386
* installing *source* package 'RBGL' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c bbc.cpp -o bbc.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cliques.cpp -o cliques.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c clusteringCoef.cpp -o clusteringCoef.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dominatorTree.cpp -o dominatorTree.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from edmonds_optimum_branching.hpp:94:0,
from edmonds_optimum_branching.cpp:3:
edmonds_optimum_branching_impl.hpp: In function 'void edmonds_optimum_branching(TEdgeListGraph&, TVertexIndexMap, TWeightMap, TInputIterator, TInputIterator, TOutputIterator)':
edmonds_optimum_branching_impl.hpp:520:71: warning: typedef 'EdgeIter' locally defined but not used [-Wunused-local-typedefs]
typedef typename graph_traits::edge_iterator EdgeIter;
^
edmonds_optimum_branching_impl.hpp:521:71: warning: typedef 'weight_t' locally defined but not used [-Wunused-local-typedefs]
typedef typename property_traits::value_type weight_t;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c hcs.cpp -o hcs.o
In file included from mincut.hpp:4:0,
from hcs.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list; OutputIterator = std::back_insert_iterator >; typename boost::graph_traits::edges_size_type = unsigned int]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
typename Traits::vertex_descriptor p;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c incrConnComp.cpp -o incrConnComp.o
In file included from incrConnComp.cpp:2:0:
incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)':
incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable]
BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/foreach.hpp:1107:14: note: in definition of macro 'BOOST_FOREACH'
for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c interfaces.cpp -o interfaces.o
interfaces.cpp: In function 'SEXPREC* BGL_tsort_D(SEXP, SEXP, SEXP)':
interfaces.cpp:57:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:61:62: warning: typedef 'Color' locally defined but not used [-Wunused-local-typedefs]
typedef property_map::type Color;
^
interfaces.cpp: In function 'SEXPREC* BGL_bfs_D(SEXP, SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:98:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:99:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_dfs_D(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:142:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:143:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_connected_components_U(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:198:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:199:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_strong_components_D(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:225:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:226:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_biconnected_components_U(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:252:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:253:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_articulation_points_U(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:295:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp: In function 'SEXPREC* BGL_edge_connectivity_U(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:320:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_sequential_vertex_coloring(SEXP, SEXP, SEXP)':
interfaces.cpp:360:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:361:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
In file included from interfaces.cpp:7:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >; typename boost::graph_traits::degree_size_type = unsigned int]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
typename Traits::vertex_descriptor p;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c minST.cpp -o minST.o
minST.cpp: In function 'SEXPREC* BGL_KMST_D(SEXP, SEXP, SEXP, SEXP)':
minST.cpp:14:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
minST.cpp: In function 'SEXPREC* BGL_KMST_U(SEXP, SEXP, SEXP, SEXP)':
minST.cpp:48:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
minST.cpp: In function 'SEXPREC* BGL_PRIM_U(SEXP, SEXP, SEXP, SEXP)':
minST.cpp:81:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from minST.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >; Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, unsigned int>, unsigned int, unsigned int&>; Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, unsigned int>, unsigned int, unsigned int&>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& ei +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from minST.cpp:2:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: '*((void*)& ei +24)' was declared here
typename graph_traits::edge_iterator ei, eiend;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:33:0,
from RBGL.hpp:38,
from minST.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/edge.hpp:27:34: warning: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
: m_source(s), m_target(d) { }
^
In file included from minST.cpp:2:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' was declared here
typename graph_traits::edge_iterator ei, eiend;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c mincut.cpp -o mincut.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from mincut.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_max_flow_internal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, E_MF_METHOD)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& ei +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
mincut.cpp:99:19: note: '*((void*)& ei +24)' was declared here
edge_iterator ei, e_end;
^
mincut.cpp:103:54: warning: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(eList)[i++] = source(*ei, flow_g);
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223:0,
from RBGL.hpp:38,
from mincut.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:152:62: warning: '*((void*)(& ei)+16).__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized]
&(*this->base()).get_property());
^
mincut.cpp:99:19: note: '*((void*)(& ei)+16).__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >::_M_current' was declared here
edge_iterator ei, e_end;
^
In file included from mincut.hpp:4:0,
from mincut.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator >; typename boost::graph_traits::edges_size_type = unsigned int]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
typename Traits::vertex_descriptor p;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ordering.cpp -o ordering.o
ordering.cpp: In function 'SEXPREC* BGL_min_degree_ordering(SEXP, SEXP, SEXP, SEXP)':
ordering.cpp:133:53: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits::vertex_descriptor Vertex;
^
ordering.cpp: In function 'SEXPREC* BGL_king_ordering(SEXP, SEXP, SEXP, SEXP)':
ordering.cpp:182:48: warning: variable 'id' set but not used [-Wunused-but-set-variable]
property_map::type id = get(vertex_index, g);
^
ordering.cpp:176:53: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits::vertex_descriptor Vertex;
^
ordering.cpp: In function 'SEXPREC* BGL_sloan_ordering(SEXP, SEXP, SEXP, SEXP, SEXP)':
ordering.cpp:232:47: warning: typedef 'Pair' locally defined but not used [-Wunused-local-typedefs]
typedef std::pair Pair;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c planar.cpp -o planar.o
planar.cpp: In function 'SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)':
planar.cpp:161:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int i = 0; i < v_vis.f_vis.size(); i++ )
^
planar.cpp:165:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int j = 0; j < v_vis.f_vis[i].size(); j++ )
^
planar.cpp: In function 'SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)':
planar.cpp:256:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int i = 0; i < ordering.size(); i++ )
^
planar.cpp: In function 'SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)':
planar.cpp:369:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int i = 0, j = 0; i < num_vertices(g); i++ )
^
planar.cpp: In function 'SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)':
planar.cpp:461:6: warning: unused variable 'i' [-Wunused-variable]
int i, j = 0;
^
In file included from planar.cpp:6:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp: In function 'void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, VertexIndexMap) [with Graph = boost::adjacency_list, boost::property >; PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator >*, std::vector > > >, boost::vec_adj_list_vertex_id_map, unsigned int> >; ForwardIterator = __gnu_cxx::__normal_iterator >; GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, unsigned int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, unsigned int>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp:217:22: warning: 'next_to_rightmost' may be used uninitialized in this function [-Wmaybe-uninitialized]
vertex_t next_to_rightmost;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12:0,
from planar.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function 'void boost::boyer_myrvold_impl::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator > >; EdgeIndexMap = boost::adj_list_edge_property_map, boost::edge_index_t>; Graph = boost::adjacency_list, boost::property >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, unsigned int>; StoreOldHandlesPolicy = boost::graph::detail::store_old_handles; StoreEmbeddingPolicy = boost::graph::detail::no_embedding]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1436:11: warning: 'bicomp_root' may be used uninitialized in this function [-Wmaybe-uninitialized]
z = kuratowski_walkup(v,
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12,
from planar.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp: In static member function 'static bool boost::maximum_cardinality_matching_verifier::verify_matching(const Graph&, MateMap, VertexIndexMap) [with Graph = R_adjacency_list; MateMap = unsigned int*; VertexIndexMap = boost::vec_adj_list_vertex_id_map, unsigned int>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:124:64: warning: '*((void*)& occ +8)' may be used uninitialized in this function [-Wmaybe-uninitialized]
bgl_named_params(T v, const Base& b) : m_value(v), m_base(b) { }
^
In file included from planar.cpp:11:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:820:48: note: '*((void*)& occ +8)' was declared here
detail::odd_components_counter occ(num_odd_components);
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c registerSigHandlers.cpp -o registerSigHandlers.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp: In function 'SEXPREC* BGL_dijkstra_shortest_paths_D(SEXP, SEXP, SEXP, SEXP, SEXP)':
shortestPath.cpp:17:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
shortestPath.cpp: In function 'SEXPREC* BGL_dag_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)':
shortestPath.cpp:136:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
shortestPath.cpp: In function 'SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXP, SEXP, SEXP, SEXP)':
shortestPath.cpp:177:81: warning: typedef 'Graph' locally defined but not used [-Wunused-local-typedefs]
property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
^
shortestPath.cpp:180:39: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef std::pair < int, int >Edge;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>; Size = unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
from shortestPath.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: '*((void*)& i +24)' was declared here
typename GTraits::edge_iterator i, end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list >; Size = int; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; PredecessorMap = unsigned int*; DistanceMap = double*; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
from shortestPath.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: '*((void*)& i +24)' was declared here
typename GTraits::edge_iterator i, end;
^
In file included from RBGL.hpp:17:0,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:129:65: warning: '*((void*)(& i)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
inline const T& get(const T* pa, std::ptrdiff_t k) { return pa[k]; }
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
from shortestPath.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: '*((void*)(& i)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' was declared here
typename GTraits::edge_iterator i, end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::floyd_warshall_all_pairs_shortest_paths(const VertexAndEdgeListGraph&, DistanceMatrix&, const WeightMap&, const BinaryPredicate&, const BinaryFunction&, const Infinity&, const Zero&) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; Zero = double]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& first +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from shortestPath.cpp:7:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:111:66: note: '*((void*)& first +24)' was declared here
typename graph_traits::edge_iterator first, last;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& ei +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
shortestPath.cpp:101:50: note: '*((void*)& ei +24)' was declared here
graph_traits< EdgeGraph >::edge_iterator ei, ei_end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& e +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from shortestPath.cpp:4:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: '*((void*)& e +24)' was declared here
typename Traits2::edge_iterator e, e_end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_array.hpp:17:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:24,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20,
from shortestPath.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
return px[i];
^
In file included from shortestPath.cpp:4:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' was declared here
typename Traits2::edge_iterator e, e_end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& e +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from shortestPath.cpp:4:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:39: note: '*((void*)& e +24)' was declared here
typename Traits1::edge_iterator e, e_end;
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:88:70: warning: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
get(id1, target(*e, g1)) + 1, g2);
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sna.cpp -o sna.o
sna.cpp: In function 'SEXPREC* lambdaSets(SEXP, SEXP, SEXP, SEXP)':
sna.cpp:161:9: warning: variable 'res_cap' set but not used [-Wunused-but-set-variable]
res_cap = get(edge_residual_capacity, flow_g);
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from sna.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>; Size = unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
from sna.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: '*((void*)& i +24)' was declared here
typename GTraits::edge_iterator i, end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from sna.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& e +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from sna.cpp:3:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: '*((void*)& e +24)' was declared here
typename Traits2::edge_iterator e, e_end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/shared_array_property_map.hpp:13:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:27,
from sna.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
return px[i];
^
In file included from sna.cpp:3:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' was declared here
typename Traits2::edge_iterator e, e_end;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c transitive_closure.cpp -o transitive_closure.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
from transitive_closure.cpp:16:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_transitive_closure_D(SEXP, SEXP, SEXP)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& ei +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
transitive_closure.cpp:43:33: note: '*((void*)& ei +24)' was declared here
Graph_dd::edge_iterator ei, e_end;
^
transitive_closure.cpp:46:50: warning: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(eList)[i++] = source(*ei, TC);
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c wavefront.cpp -o wavefront.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o RBGL.dll tmp.def bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o registerSigHandlers.o shortestPath.o sna.o transitive_closure.o wavefront.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/RBGL.buildbin-libdir/00LOCK-RBGL/00new/RBGL/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RBGL'
finding HTML links ... done
FileDep html
RBGL.overview html
astarSearch html
bandwidth html
bccluster html
bellman.ford.sp html
betweenness html
bfs html
biConnComp html
boyerMyrvoldPlanarityTest html
chrobakPayneStraightLineDrawing html
clusteringCoef html
clusteringCoefAppr html
coloring html
connectedComp html
dag.sp html
defunct html
dijkstra.sp html
dominatorTree html
edgeConn html
edmondsMaxCardinalityMatching html
edmondsOptimumBranching html
extractPath html
floyd.warshall.all.pairs.sp html
gprofile html
graphGenerator html
highlyConnSG html
incrConnComp html
is.triangulated html
isKuratowskiSubgraph html
isStraightLineDrawing html
isomorphism html
johnson.all.pairs.sp html
kCliques html
kCores html
lambdaSets html
layout html
makeBiconnectedPlanar html
makeConnected html
makeMaximalPlanar html
maxClique html
maxFlow html
maximumCycleRatio html
minCut html
minimumCycleRatio html
mstree.kruskal html
mstree.prim html
ordering html
planarCanonicalOrdering html
planarFaceTraversal html
removeSelfLoops html
separates html
sloanStartEndVertices html
sp.between html
strongComp html
transClosure html
transitivity html
tsort html
wavefront html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'RBGL' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c bbc.cpp -o bbc.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cliques.cpp -o cliques.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c clusteringCoef.cpp -o clusteringCoef.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dominatorTree.cpp -o dominatorTree.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from edmonds_optimum_branching.hpp:94:0,
from edmonds_optimum_branching.cpp:3:
edmonds_optimum_branching_impl.hpp: In function 'void edmonds_optimum_branching(TEdgeListGraph&, TVertexIndexMap, TWeightMap, TInputIterator, TInputIterator, TOutputIterator)':
edmonds_optimum_branching_impl.hpp:520:71: warning: typedef 'EdgeIter' locally defined but not used [-Wunused-local-typedefs]
typedef typename graph_traits::edge_iterator EdgeIter;
^
edmonds_optimum_branching_impl.hpp:521:71: warning: typedef 'weight_t' locally defined but not used [-Wunused-local-typedefs]
typedef typename property_traits::value_type weight_t;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c hcs.cpp -o hcs.o
In file included from mincut.hpp:4:0,
from hcs.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list; OutputIterator = std::back_insert_iterator >; typename boost::graph_traits::edges_size_type = long long unsigned int]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
typename Traits::vertex_descriptor p;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c incrConnComp.cpp -o incrConnComp.o
In file included from incrConnComp.cpp:2:0:
incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)':
incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable]
BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/foreach.hpp:1107:14: note: in definition of macro 'BOOST_FOREACH'
for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c interfaces.cpp -o interfaces.o
interfaces.cpp: In function 'SEXPREC* BGL_tsort_D(SEXP, SEXP, SEXP)':
interfaces.cpp:57:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:61:62: warning: typedef 'Color' locally defined but not used [-Wunused-local-typedefs]
typedef property_map::type Color;
^
interfaces.cpp: In function 'SEXPREC* BGL_bfs_D(SEXP, SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:98:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:99:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_dfs_D(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:142:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:143:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_connected_components_U(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:198:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:199:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_strong_components_D(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:225:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:226:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_biconnected_components_U(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:252:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:253:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_articulation_points_U(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:295:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp: In function 'SEXPREC* BGL_edge_connectivity_U(SEXP, SEXP, SEXP, SEXP)':
interfaces.cpp:320:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp: In function 'SEXPREC* BGL_sequential_vertex_coloring(SEXP, SEXP, SEXP)':
interfaces.cpp:360:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:361:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
In file included from interfaces.cpp:7:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >; typename boost::graph_traits::degree_size_type = long long unsigned int]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
typename Traits::vertex_descriptor p;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c minST.cpp -o minST.o
minST.cpp: In function 'SEXPREC* BGL_KMST_D(SEXP, SEXP, SEXP, SEXP)':
minST.cpp:14:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
minST.cpp: In function 'SEXPREC* BGL_KMST_U(SEXP, SEXP, SEXP, SEXP)':
minST.cpp:48:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
minST.cpp: In function 'SEXPREC* BGL_PRIM_U(SEXP, SEXP, SEXP, SEXP)':
minST.cpp:81:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from minST.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >; Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long long unsigned int>, long long unsigned int, long long unsigned int&>; Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long long unsigned int>, long long unsigned int, long long unsigned int&>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& ei +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from minST.cpp:2:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: '*((void*)& ei +48)' was declared here
typename graph_traits::edge_iterator ei, eiend;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:33:0,
from RBGL.hpp:38,
from minST.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/edge.hpp:27:34: warning: '*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
: m_source(s), m_target(d) { }
^
In file included from minST.cpp:2:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: '*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' was declared here
typename graph_traits::edge_iterator ei, eiend;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c mincut.cpp -o mincut.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from mincut.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_max_flow_internal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, E_MF_METHOD)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& ei +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
mincut.cpp:99:19: note: '*((void*)& ei +48)' was declared here
edge_iterator ei, e_end;
^
mincut.cpp:103:54: warning: '*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(eList)[i++] = source(*ei, flow_g);
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223:0,
from RBGL.hpp:38,
from mincut.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:152:62: warning: '*((void*)(& ei)+32).__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized]
&(*this->base()).get_property());
^
mincut.cpp:99:19: note: '*((void*)(& ei)+32).__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >::_M_current' was declared here
edge_iterator ei, e_end;
^
In file included from mincut.hpp:4:0,
from mincut.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator >; typename boost::graph_traits::edges_size_type = long long unsigned int]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
typename Traits::vertex_descriptor p;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ordering.cpp -o ordering.o
ordering.cpp: In function 'SEXPREC* BGL_min_degree_ordering(SEXP, SEXP, SEXP, SEXP)':
ordering.cpp:133:53: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits::vertex_descriptor Vertex;
^
ordering.cpp: In function 'SEXPREC* BGL_king_ordering(SEXP, SEXP, SEXP, SEXP)':
ordering.cpp:182:48: warning: variable 'id' set but not used [-Wunused-but-set-variable]
property_map::type id = get(vertex_index, g);
^
ordering.cpp:176:53: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits::vertex_descriptor Vertex;
^
ordering.cpp: In function 'SEXPREC* BGL_sloan_ordering(SEXP, SEXP, SEXP, SEXP, SEXP)':
ordering.cpp:232:47: warning: typedef 'Pair' locally defined but not used [-Wunused-local-typedefs]
typedef std::pair Pair;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c planar.cpp -o planar.o
planar.cpp: In function 'SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)':
planar.cpp:161:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int i = 0; i < v_vis.f_vis.size(); i++ )
^
planar.cpp:165:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int j = 0; j < v_vis.f_vis[i].size(); j++ )
^
planar.cpp: In function 'SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)':
planar.cpp:256:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int i = 0; i < ordering.size(); i++ )
^
planar.cpp: In function 'SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)':
planar.cpp:369:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int i = 0, j = 0; i < num_vertices(g); i++ )
^
planar.cpp: In function 'SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)':
planar.cpp:461:6: warning: unused variable 'i' [-Wunused-variable]
int i, j = 0;
^
In file included from planar.cpp:6:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp: In function 'void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, VertexIndexMap) [with Graph = boost::adjacency_list, boost::property >; PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator >*, std::vector > > >, boost::vec_adj_list_vertex_id_map, long long unsigned int> >; ForwardIterator = __gnu_cxx::__normal_iterator >; GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long long unsigned int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long long unsigned int>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp:217:22: warning: 'next_to_rightmost' may be used uninitialized in this function [-Wmaybe-uninitialized]
vertex_t next_to_rightmost;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12:0,
from planar.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function 'void boost::boyer_myrvold_impl::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator > >; EdgeIndexMap = boost::adj_list_edge_property_map, boost::edge_index_t>; Graph = boost::adjacency_list, boost::property >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long long unsigned int>; StoreOldHandlesPolicy = boost::graph::detail::store_old_handles; StoreEmbeddingPolicy = boost::graph::detail::no_embedding]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1436:11: warning: 'bicomp_root' may be used uninitialized in this function [-Wmaybe-uninitialized]
z = kuratowski_walkup(v,
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12,
from planar.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp: In static member function 'static bool boost::maximum_cardinality_matching_verifier::verify_matching(const Graph&, MateMap, VertexIndexMap) [with Graph = R_adjacency_list; MateMap = long long unsigned int*; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long long unsigned int>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:124:64: warning: '*((void*)& occ +16)' may be used uninitialized in this function [-Wmaybe-uninitialized]
bgl_named_params(T v, const Base& b) : m_value(v), m_base(b) { }
^
In file included from planar.cpp:11:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:820:48: note: '*((void*)& occ +16)' was declared here
detail::odd_components_counter occ(num_odd_components);
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c registerSigHandlers.cpp -o registerSigHandlers.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp: In function 'SEXPREC* BGL_dijkstra_shortest_paths_D(SEXP, SEXP, SEXP, SEXP, SEXP)':
shortestPath.cpp:17:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
shortestPath.cpp: In function 'SEXPREC* BGL_dag_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)':
shortestPath.cpp:136:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
shortestPath.cpp: In function 'SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXP, SEXP, SEXP, SEXP)':
shortestPath.cpp:177:81: warning: typedef 'Graph' locally defined but not used [-Wunused-local-typedefs]
property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
^
shortestPath.cpp:180:39: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef std::pair < int, int >Edge;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>; Size = long long unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& i +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
from shortestPath.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: '*((void*)& i +48)' was declared here
typename GTraits::edge_iterator i, end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list >; Size = int; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; PredecessorMap = long long unsigned int*; DistanceMap = double*; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& i +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
from shortestPath.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: '*((void*)& i +48)' was declared here
typename GTraits::edge_iterator i, end;
^
In file included from RBGL.hpp:17:0,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:129:65: warning: '*((void*)(& i)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
inline const T& get(const T* pa, std::ptrdiff_t k) { return pa[k]; }
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
from shortestPath.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: '*((void*)(& i)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' was declared here
typename GTraits::edge_iterator i, end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::floyd_warshall_all_pairs_shortest_paths(const VertexAndEdgeListGraph&, DistanceMatrix&, const WeightMap&, const BinaryPredicate&, const BinaryFunction&, const Infinity&, const Zero&) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; Zero = double]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& first +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from shortestPath.cpp:7:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:111:66: note: '*((void*)& first +48)' was declared here
typename graph_traits::edge_iterator first, last;
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:125:12: warning: '*((void*)(& first)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (d[source(*first, g)][target(*first, g)] != inf) {
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& ei +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
shortestPath.cpp:101:50: note: '*((void*)& ei +48)' was declared here
graph_traits< EdgeGraph >::edge_iterator ei, ei_end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, long long unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& e +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from shortestPath.cpp:4:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: '*((void*)& e +48)' was declared here
typename Traits2::edge_iterator e, e_end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_array.hpp:17:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:24,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20,
from shortestPath.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: '*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
return px[i];
^
In file included from shortestPath.cpp:4:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: '*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' was declared here
typename Traits2::edge_iterator e, e_end;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from shortestPath.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& e +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
^
In file included from shortestPath.cpp:4:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:39: note: '*((void*)& e +48)' was declared here
typename Traits1::edge_iterator e, e_end;
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:88:70: warning: '*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long long unsigned int, boost::detail::edge_desc_impl, long long int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized]
get(id1, target(*e, g1)) + 1, g2);
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sna.cpp -o sna.o
sna.cpp: In function 'SEXPREC* lambdaSets(SEXP, SEXP, SEXP, SEXP)':
sna.cpp:161:9: warning: variable 'res_cap' set but not used [-Wunused-but-set-variable]
res_cap = get(edge_residual_capacity, flow_g);
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
from RBGL.hpp:38,
from sna.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list 