Package: RBGL

Version: 1.20.0

Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD check --no-vignettes RBGL_1.20.0.tar.gz

StartedAt: 2009-10-20 17:36:34 -0700 (Tue, 20 Oct 2009)

EndedAt: 2009-10-20 17:37:50 -0700 (Tue, 20 Oct 2009)

EllapsedTime: 76.3 seconds

RetCode: 0

Status: OK

CheckDir: RBGL.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/RBGL.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.20.0'
* checking package name space information ... OK
* 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 files against version 2 parser ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c bbc.cpp -o bbc.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from bbc.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'void boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<G>::vertex_descriptor, PredecessorMap, DistanceMap, WeightMap, IndexMap, Compare, Combine, DistZero, DijkstraVisitor, 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>, DijkstraVisitor = 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 long unsigned int*, std::vector<long long unsigned int, std::allocator<long 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 long unsigned int, long long unsigned int&> >, PredecessorMap = boost::dummy_property_map, 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>, Compare = std::less<double>, Combine = boost::closed_plus<double>, DistZero = double, 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:81: warning: 'bfs_vis.boost::detail::dijkstra_bfs_visitor<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 long unsigned int*, std::vector<long long unsigned int, std::allocator<long 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 long unsigned int, long long unsigned int&> >, boost::relaxed_heap<long unsigned int, boost::indirect_cmp<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&>, std::less<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> >, 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::dummy_property_map, 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::closed_plus<double>, std::less<double> >::m_decreased' may be used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:205: note: 'bfs_vis.boost::detail::dijkstra_bfs_visitor<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 long unsigned int*, std::vector<long long unsigned int, std::allocator<long 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 long unsigned int, long long unsigned int&> >, boost::relaxed_heap<long unsigned int, boost::indirect_cmp<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&>, std::less<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> >, 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::dummy_property_map, 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::closed_plus<double>, std::less<double> >::m_decreased' was declared here
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c cliques.cpp -o cliques.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from cliques.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c clusteringCoef.cpp -o clusteringCoef.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from clusteringCoef.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
clusteringCoef.cpp: In function 'SEXPREC* graphGenerator(SEXPREC*, SEXPREC*, SEXPREC*)':
clusteringCoef.cpp:394: warning: 'u' may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c dominatorTree.cpp -o dominatorTree.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from dominatorTree.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c hcs.cpp -o hcs.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from hcs.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c incrConnComp.cpp -o incrConnComp.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from incrConnComp.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c interfaces.cpp -o interfaces.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from interfaces.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c layout.cpp -o layout.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from layout.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
layout.cpp: In function 'SEXPREC* BGL_layout_internal(E_LAYOUT_METHOD, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
layout.cpp:116: warning: unused variable 'r'
layout.cpp:117: warning: unused variable 'w'
layout.cpp:118: warning: unused variable 'h'
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::vec_adj_list_vertex_property_map<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::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::simple_point<double>, boost::simple_point<double>&, vertex_position_t>, Dim = double, AttractiveForce = boost::square_distance_attractive_force, RepulsiveForce = boost::square_distance_repulsive_force, ForcePairs = boost::grid_force_pairs<double, boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<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::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::simple_point<double>, boost::simple_point<double>&, vertex_position_t> >, 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>&>]':
fruchterman_reingold.hpp:423:   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::vec_adj_list_vertex_property_map<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::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::simple_point<double>, boost::simple_point<double>&, vertex_position_t>, Dim = double, AttractiveForce = boost::square_distance_attractive_force, RepulsiveForce = boost::square_distance_repulsive_force, ForcePairs = boost::grid_force_pairs<double, boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<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::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::simple_point<double>, boost::simple_point<double>&, vertex_position_t> >, Cooling = boost::linear_cooling<double>, Param = boost::square_distance_attractive_force, Tag = boost::attractive_force_t, Rest = boost::no_property]'
fruchterman_reingold.hpp:449:   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::vec_adj_list_vertex_property_map<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::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::simple_point<double>, boost::simple_point<double>&, vertex_position_t>, Dim = double, Param = boost::square_distance_attractive_force, Tag = boost::attractive_force_t, Rest = boost::no_property]'
fruchterman_reingold.hpp:470:   instantiated from 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim) [with Graph = IndexGraph, PositionMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<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::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::simple_point<double>, boost::simple_point<double>&, vertex_position_t>, Dim = double]'
layout.cpp:112:   instantiated from here
fruchterman_reingold.hpp:354: warning: suggest parentheses around assignment used as truth value
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'void boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<G>::vertex_descriptor, PredecessorMap, DistanceMap, WeightMap, IndexMap, Compare, Combine, DistZero, DijkstraVisitor, ColorMap) [with VertexListGraph = 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>, DijkstraVisitor = boost::dijkstra_visitor<boost::null_visitor>, PredecessorMap = boost::dummy_property_map, DistanceMap = boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, IndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int>, Compare = std::less<double>, Combine = boost::closed_plus<double>, DistZero = double, ColorMap = boost::iterator_property_map<boost::default_color_type*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:81: warning: 'bfs_vis.boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long unsigned int, boost::indirect_cmp<boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, std::less<double> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, boost::dummy_property_map, boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, boost::closed_plus<double>, std::less<double> >::m_decreased' may be used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:205: note: 'bfs_vis.boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long unsigned int, boost::indirect_cmp<boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, std::less<double> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, boost::dummy_property_map, boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, boost::closed_plus<double>, std::less<double> >::m_decreased' was declared here
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c minST.cpp -o minST.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from minST.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c mincut.cpp -o mincut.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from mincut.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c ordering.cpp -o ordering.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from ordering.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c shortestPath.cpp -o shortestPath.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from shortestPath.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'void boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<G>::vertex_descriptor, PredecessorMap, DistanceMap, WeightMap, IndexMap, Compare, Combine, DistZero, DijkstraVisitor, ColorMap) [with VertexListGraph = 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>, DijkstraVisitor = boost::dijkstra_visitor<boost::null_visitor>, PredecessorMap = boost::dummy_property_map, DistanceMap = boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, IndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int>, Compare = std::less<double>, Combine = boost::closed_plus<double>, DistZero = double, ColorMap = boost::iterator_property_map<boost::default_color_type*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:81: warning: 'bfs_vis.boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long unsigned int, boost::indirect_cmp<boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, std::less<double> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, boost::dummy_property_map, boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, boost::closed_plus<double>, std::less<double> >::m_decreased' may be used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:205: note: 'bfs_vis.boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long unsigned int, boost::indirect_cmp<boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, std::less<double> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, boost::dummy_property_map, boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, boost::closed_plus<double>, std::less<double> >::m_decreased' was declared here
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c sna.cpp -o sna.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from sna.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'void boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<G>::vertex_descriptor, PredecessorMap, DistanceMap, WeightMap, IndexMap, Compare, Combine, DistZero, DijkstraVisitor, ColorMap) [with VertexListGraph = 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>, DijkstraVisitor = boost::dijkstra_visitor<boost::null_visitor>, PredecessorMap = boost::dummy_property_map, DistanceMap = boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, IndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int>, Compare = std::less<double>, Combine = boost::closed_plus<double>, DistZero = double, ColorMap = boost::iterator_property_map<boost::default_color_type*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:81: warning: 'bfs_vis.boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long unsigned int, boost::indirect_cmp<boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, std::less<double> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, boost::dummy_property_map, boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, boost::closed_plus<double>, std::less<double> >::m_decreased' may be used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:205: note: 'bfs_vis.boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long unsigned int, boost::indirect_cmp<boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, std::less<double> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_distance_t, double, boost::no_property>, long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight2_t>, boost::dummy_property_map, boost::vec_adj_list_vertex_property_map<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::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>*, double, double&, boost::vertex_distance_t>, boost::closed_plus<double>, std::less<double> >::m_decreased' was declared here
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c transitive_closure.cpp -o transitive_closure.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from transitive_closure.cpp:16:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c wavefront.cpp -o wavefront.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:26,
                 from wavefront.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -shared -L/usr/local/lib64 -o RBGL.so bbc.o cliques.o clusteringCoef.o dominatorTree.o hcs.o incrConnComp.o interfaces.o layout.o minST.o mincut.o ordering.o shortestPath.o sna.o transitive_closure.o wavefront.o -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
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** building package indices ...
* DONE (RBGL)