Package: RBGL

Version: 1.13.1

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check RBGL_1.13.1.tar.gz

RetCode: 0

Time: 102.9 seconds

Status: OK

CheckDir: RBGL.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/RBGL.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-04-17 r41210)
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.13.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RBGL' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating RBGL-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating RBGL-manual.tex ... OK
* checking RBGL-manual.tex ... OK

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c bbc.cpp -o bbc.o
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'void boost::detail::dijkstra_dispatch2(const VertexListGraph&, typename boost::graph_traits<G>::vertex_descriptor, DistanceMap, WeightMap, IndexMap, const Params&, ColorMap) [with VertexListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::no_property, boost::listS>, DistanceMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, long unsigned int>, double, double&>, WeightMap = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::edge_weight_t>, IndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, long unsigned int>, Params = boost::bgl_named_params<boost::detail::graph::brandes_dijkstra_visitor<const boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::no_property, boost::listS>, boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::edge_weight_t>, boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >, std::allocator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > > > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >&>, boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, long unsigned int>, double, double&>, boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int, std::allocator<long unsigned int> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, long unsigned int>, long unsigned int, long unsigned int&> >, boost::graph_visitor_t, boost::bgl_named_params<boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, long unsigned int>, double, double&>, boost::vertex_distance_t, boost::bgl_named_params<boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, long unsigned int>, boost::vertex_index_t, boost::bgl_named_params<boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::edge_weight_t>, boost::edge_weight_t, boost::no_property> > > >, ColorMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::default_color_type*, std::vector<boost::default_color_type, std::allocator<boost::default_color_type> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:80: warning: 'bfs_vis$m_decreased' is used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c cliques.cpp -o cliques.o
cliques.cpp: In function 'void print_one_clique(oneCliqueType&)':
cliques.cpp:110: warning: comparison between signed and unsigned integer expressions
cliques.cpp: In function 'void print_all_cliques(allCliquesType&, char*)':
cliques.cpp:118: warning: comparison between signed and unsigned integer expressions
cliques.cpp: In function 'void extend_v2(Graph_ud&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, int, int, int&, allCliquesType&)':
cliques.cpp:139: warning: 's' may be used uninitialized in this function
cliques.cpp:139: warning: 'pos' may be used uninitialized in this function
cliques.cpp:138: warning: 'fixp' may be used uninitialized in this function
cliques.cpp: At global scope:
cliques.cpp:115: warning: 'void print_all_cliques(allCliquesType&, char*)' defined but not used
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c clusteringCoef.cpp -o clusteringCoef.o
clusteringCoef.cpp: In function 'int findIndex(int, const std::vector<int, std::allocator<int> >&)':
clusteringCoef.cpp:132: warning: comparison between signed and unsigned integer expressions
clusteringCoef.cpp: In function 'SEXPREC* clusteringCoefAppr(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
clusteringCoef.cpp:248: warning: 'w' may be used uninitialized in this function
clusteringCoef.cpp:248: warning: 'u' may be used uninitialized in this function
clusteringCoef.cpp: In function 'SEXPREC* graphGenerator(SEXPREC*, SEXPREC*, SEXPREC*)':
clusteringCoef.cpp:394: warning: 'w' may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c hcs.cpp -o hcs.o
hcs.cpp: In function 'void output_graph_labels(const V_Label&, const char*)':
hcs.cpp:27: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function 'void build_subgraph(Cluster&, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)':
hcs.cpp:62: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function 'void remove_vertices(int, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)':
hcs.cpp:117: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function 'dst cluster_distance(const Graph_ud&, V_Label&, int, V_Label&)':
hcs.cpp:134: warning: comparison between signed and unsigned integer expressions
hcs.cpp:138: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function 'void adopt_singleton(const Graph_ud&, V_Label&, ClusterResult&)':
hcs.cpp:206: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function 'void remove_clusters(ClusterResult&, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)':
hcs.cpp:248: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function 'void HCS_internal(const Graph_ud&, V_Label&, ClusterResult&)':
hcs.cpp:288: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function 'SEXPREC* HCS_loop(Graph_ud&, V_Label&)':
hcs.cpp:363: warning: comparison between signed and unsigned integer expressions
hcs.cpp:393: warning: comparison between signed and unsigned integer expressions
hcs.cpp:397: warning: comparison between signed and unsigned integer expressions
hcs.cpp:353: warning: unused variable 'found_new_cluster'
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'typename boost::graph_traits<G>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list<boost::undirectedS, double>, OutputIterator = std::back_insert_iterator<std::vector<long unsigned int, std::allocator<long unsigned int> > >]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D96599$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D96599$D96564$m_value$D94361$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D96599$D96564$m_value$D94361$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D96599$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D96599$D96564$m_value$D94361$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D96599$D96564$m_value$D94361$m_source' is used uninitialized in this function
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: 'p' may be used uninitialized in this function
hcs.cpp: At global scope:
hcs.cpp:24: warning: 'void output_graph_labels(const V_Label&, const char*)' defined but not used
hcs.cpp:32: warning: 'void output_graph(const Graph_ud&, const char*)' defined but not used
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXPREC*, SEXPREC*, SEXPREC*, E_IC_METHOD)':
incrConnComp.cpp:67: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c interfaces.cpp -o interfaces.o
interfaces.cpp: In function 'SEXPREC* BGL_articulation_points_U(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
interfaces.cpp:310: warning: comparison between signed and unsigned integer expressions
interfaces.cpp: In function 'SEXPREC* BGL_astar_search_D(SEXPREC*, SEXPREC*, SEXPREC*)':
interfaces.cpp:405: warning: 'ansList' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'typename boost::graph_traits<G>::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = Graph_ud, OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > > >]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D101129$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D101129$D101094$m_value$D81041$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D101129$D101094$m_value$D81041$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D101129$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D101129$D101094$m_value$D81041$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D101129$D101094$m_value$D81041$m_source' is used uninitialized in this function
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: 'p' may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c layout.cpp -o layout.o
layout.cpp: In function 'SEXPREC* BGL_gursov_atun_layout(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
layout.cpp:219: warning: unused variable 'w'
layout.cpp:220: warning: unused variable 'h'
boostIncl/boost/graph/fruchterman_reingold.hpp: In function 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim, AttractiveForce, RepulsiveForce, ForcePairs, Cooling, DisplacementMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>, PositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::simple_point<double>*, std::vector<boost::simple_point<double>, std::allocator<boost::simple_point<double> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, long unsigned int>, boost::simple_point<double>, boost::simple_point<double>&>, Dim = double, AttractiveForce = boost::square_distance_attractive_force, RepulsiveForce = boost::square_distance_repulsive_force, ForcePairs = boost::grid_force_pairs<double, boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::simple_point<double>*, std::vector<boost::simple_point<double>, std::allocator<boost::simple_point<double> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, long unsigned int>, boost::simple_point<double>, boost::simple_point<double>&> >, Cooling = boost::linear_cooling<double>, DisplacementMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::simple_point<double>*, std::vector<boost::simple_point<double>, std::allocator<boost::simple_point<double> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, long unsigned int>, boost::simple_point<double>, boost::simple_point<double>&>]':
boostIncl/boost/graph/fruchterman_reingold.hpp:366:   instantiated from 'static void boost::detail::fr_force_directed_layout<boost::detail::error_property_not_found>::run(const Graph&, PositionMap, Dim, Dim, AttractiveForce, RepulsiveForce, ForcePairs, Cooling, boost::detail::error_property_not_found, const boost::bgl_named_params<Param, Tag, Rest>&) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>, PositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::simple_point<double>*, std::vector<boost::simple_point<double>, std::allocator<boost::simple_point<double> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, long unsigned int>, boost::simple_point<double>, boost::simple_point<double>&>, Dim = double, AttractiveForce = boost::square_distance_attractive_force, RepulsiveForce = boost::square_distance_repulsive_force, ForcePairs = boost::grid_force_pairs<double, boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::simple_point<double>*, std::vector<boost::simple_point<double>, std::allocator<boost::simple_point<double> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, long unsigned int>, boost::simple_point<double>, boost::simple_point<double>&> >, Cooling = boost::linear_cooling<double>, Param = boost::square_distance_attractive_force, Tag = boost::attractive_force_t, Rest = boost::no_property]'
boostIncl/boost/graph/fruchterman_reingold.hpp:392:   instantiated from 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim, const boost::bgl_named_params<P, T, R>&) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>, PositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::simple_point<double>*, std::vector<boost::simple_point<double>, std::allocator<boost::simple_point<double> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, long unsigned int>, boost::simple_point<double>, boost::simple_point<double>&>, Dim = double, Param = boost::square_distance_attractive_force, Tag = boost::attractive_force_t, Rest = boost::no_property]'
boostIncl/boost/graph/fruchterman_reingold.hpp:413:   instantiated from 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim) [with Graph = IndexGraph, PositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::simple_point<double>*, std::vector<boost::simple_point<double>, std::allocator<boost::simple_point<double> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, long unsigned int>, boost::simple_point<double>, boost::simple_point<double>&>, Dim = double]'
layout.cpp:187:   instantiated from here
boostIncl/boost/graph/fruchterman_reingold.hpp:312: warning: suggest parentheses around assignment used as truth value
/usr/include/c++/4.1.0/ext/new_allocator.h: In function 'std::pair<typename Config::edge_descriptor, bool> boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, boost::vec_adj_list_impl<G, C, B>&) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>, Config = boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>::config, Base = boost::undirected_graph_helper<boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>::config>]':
/usr/include/c++/4.1.0/ext/new_allocator.h:104: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'std::pair<typename Config::edge_descriptor, bool> boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, boost::vec_adj_list_impl<G, C, B>&) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, Config = boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>::config, Base = boost::directed_graph_helper<boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>::config>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D107324$m_value' is used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, DistanceZero) [with VertexAndEdgeListGraph = const boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>, DistanceMatrix = __gnu_cxx::__normal_iterator<std::vector<double, std::allocator<double> >*, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > >, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double>, boost::no_property> >, long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, DistanceZero = double]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:80: warning: 'bfs_vis$m_decreased' is used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c mincut.cpp -o mincut.o
boostIncl/boost/graph/push_relabel_max_flow.hpp: In member function 'void boost::detail::push_relabel<Graph, EdgeCapacityMap, ResidualCapacityEdgeMap, ReverseEdgeMap, VertexIndexMap, FlowValue>::discharge(typename boost::graph_traits<Graph>::vertex_descriptor) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::no_property, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::no_property> > >, boost::no_property, boost::listS>, EdgeCapacityMap = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long unsigned int, const boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::no_property> > >, boost::edge_capacity_t>, ResidualCapacityEdgeMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::no_property> > >, boost::edge_residual_capacity_t>, ReverseEdgeMap = boost::adj_list_edge_property_map<boost::directed_tag, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, const boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>&, long unsigned int, const boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::no_property> > >, boost::edge_reverse_t>, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::no_property, long unsigned int>, FlowValue = double]':
boostIncl/boost/graph/push_relabel_max_flow.hpp:340: warning: 'min_edge_iter$m_src' may be used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'SEXPREC* BGL_max_flow_internal(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, E_MF_METHOD)':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D80085$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D80085$D80050$m_value$D77681$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D80085$D80050$m_value$D77681$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D80085$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D80085$D80050$m_value$D77681$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D80085$D80050$m_value$D77681$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'typename boost::graph_traits<G>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = Graph_ud, OutputIterator = std::back_insert_iterator<std::vector<long unsigned int, std::allocator<long unsigned int> > >]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D94232$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D94232$D94197$m_value$D77681$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D94232$D94197$m_value$D77681$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D94232$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D94232$D94197$m_value$D77681$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D94232$D94197$m_value$D77681$m_source' is used uninitialized in this function
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: 'p' may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c minST.cpp -o minST.o
minST.cpp: In function 'SEXPREC* BGL_PRIM_U(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
minST.cpp:99: warning: comparison between signed and unsigned integer expressions
minST.cpp:103: warning: comparison between signed and unsigned integer expressions
minST.cpp:93: warning: unused variable 'vlist'
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c ordering.cpp -o ordering.o
ordering.cpp: In function 'SEXPREC* BGL_king_ordering(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
ordering.cpp:172: warning: unused variable 'delta'
boostIncl/boost/graph/detail/adjacency_list.hpp: In member function 'void boost::detail::mmd_impl<Graph, DegreeMap, InversePermutationMap, PermutationMap, SuperNodeMap, VertexIndexMap>::eliminate(typename boost::graph_traits<Graph>::vertex_descriptor) [with Graph = R_adjacency_list<boost::directedS, double>, DegreeMap = boost::iterator_property_map<int*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long unsigned int>, int, int&>, InversePermutationMap = int*, PermutationMap = int*, SuperNodeMap = boost::iterator_property_map<int*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long unsigned int>, int, int&>, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long unsigned int>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
shortestPath.cpp:79: warning: unused variable 'j'
shortestPath.cpp: In function 'SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
shortestPath.cpp:180: warning: unused variable 'V'
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>, DistanceMatrix = Basic2DMatrix<double>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, DistanceZero = double]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D100280$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D100280$m_value' is used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:80: warning: 'bfs_vis$m_decreased' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c sna.cpp -o sna.o
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'std::pair<typename Config::edge_descriptor, bool> boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, boost::vec_adj_list_impl<G, C, B>&) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, Config = boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>::config, Base = boost::directed_graph_helper<boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>::config>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D101387$m_value' is used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>, DistanceMatrix = Basic2DMatrix<double>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, DistanceZero = double]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:80: warning: 'bfs_vis$m_decreased' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'SEXPREC* lambdaSets(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D87959$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D87959$D87924$m_value$D86263$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D87959$D87924$m_value$D86263$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D87959$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D87959$D87924$m_value$D86263$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D87959$D87924$m_value$D86263$m_source' is used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c transitive_closure.cpp -o transitive_closure.o
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'void boost::transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap) [with Graph = R_adjacency_list<boost::directedS, double>, GraphTC = R_adjacency_list<boost::directedS, double>, G_to_TC_VertexMap = boost::iterator_property_map<long unsigned int*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long unsigned int>, long unsigned int, long unsigned int&>, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long unsigned int>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In member function 'void boost::EdgeMutableGraphConcept<G>::constraints() [with G = R_adjacency_list<boost::directedS, double>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c wavefront.cpp -o wavefront.o
g++ -shared -L/usr/local/lib64 -o RBGL.so bbc.o cliques.o clusteringCoef.o hcs.o incrConnComp.o interfaces.o layout.o mincut.o minST.o ordering.o shortestPath.o sna.o transitive_closure.o wavefront.o   -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
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