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Package 301/389HostnameOS / ArchBUILDCHECKBUILD BIN
RBGL 1.24.0
Li Long
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/RBGL
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: RBGL
Version: 1.24.0
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings RBGL_1.24.0.tar.gz
StartedAt: 2010-10-04 18:16:53 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 18:18:52 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 119.1 seconds
RetCode: 0
Status:  OK  
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/RBGL.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.24.0'
* 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 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
prepare_Rd: astarSearch.Rd:14-15: Dropping empty section \value
prepare_Rd: astarSearch.Rd:27: Dropping empty section \seealso
prepare_Rd: bandwidth.Rd:36: Dropping empty section \seealso
prepare_Rd: biConnComp.Rd:52: Dropping empty section \seealso
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:16-17: Dropping empty section \details
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:19-20: Dropping empty section \value
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:33-34: Dropping empty section \examples
prepare_Rd: chrobakPayneStraightLineDrawing.Rd:16-17: Dropping empty section \details
prepare_Rd: chrobakPayneStraightLineDrawing.Rd:19-20: Dropping empty section \value
prepare_Rd: coloring.Rd:42: Dropping empty section \seealso
prepare_Rd: dominatorTree.Rd:37: Dropping empty section \seealso
prepare_Rd: edmondsMaxCardinalityMatching.Rd:16-17: Dropping empty section \details
prepare_Rd: edmondsMaxCardinalityMatching.Rd:19-20: Dropping empty section \value
prepare_Rd: edmondsOptimumBranching.Rd:20-21: Dropping empty section \value
prepare_Rd: gprofile.Rd:37: Dropping empty section \seealso
prepare_Rd: is.triangulated.Rd:43: Dropping empty section \seealso
prepare_Rd: isKuratowskiSubgraph.Rd:16-17: Dropping empty section \details
prepare_Rd: isKuratowskiSubgraph.Rd:19-20: Dropping empty section \value
prepare_Rd: isStraightLineDrawing.Rd:17-18: Dropping empty section \details
prepare_Rd: isStraightLineDrawing.Rd:20-21: Dropping empty section \value
prepare_Rd: isomorphism.Rd:42: Dropping empty section \seealso
prepare_Rd: johnson.all.pairs.sp.Rd:34: Dropping empty section \note
prepare_Rd: kCliques.Rd:45: Dropping empty section \seealso
prepare_Rd: kCores.Rd:39: Dropping empty section \seealso
prepare_Rd: lambdaSets.Rd:45: Dropping empty section \seealso
prepare_Rd: makeBiconnectedPlanar.Rd:16-17: Dropping empty section \details
prepare_Rd: makeBiconnectedPlanar.Rd:19-20: Dropping empty section \value
prepare_Rd: makeConnected.Rd:16-17: Dropping empty section \details
prepare_Rd: makeConnected.Rd:19-20: Dropping empty section \value
prepare_Rd: makeMaximalPlanar.Rd:16-17: Dropping empty section \details
prepare_Rd: makeMaximalPlanar.Rd:19-20: Dropping empty section \value
prepare_Rd: maxClique.Rd:35: Dropping empty section \seealso
prepare_Rd: maximumCycleRatio.Rd:16-17: Dropping empty section \details
prepare_Rd: maximumCycleRatio.Rd:19-20: Dropping empty section \value
prepare_Rd: maximumCycleRatio.Rd:33-34: Dropping empty section \examples
prepare_Rd: minimumCycleRatio.Rd:16-17: Dropping empty section \details
prepare_Rd: minimumCycleRatio.Rd:19-20: Dropping empty section \value
prepare_Rd: minimumCycleRatio.Rd:33-34: Dropping empty section \examples
prepare_Rd: ordering.Rd:77: Dropping empty section \seealso
prepare_Rd: planarCanonicalOrdering.Rd:16-17: Dropping empty section \details
prepare_Rd: planarCanonicalOrdering.Rd:19-20: Dropping empty section \value
prepare_Rd: planarFaceTraversal.Rd:16-17: Dropping empty section \details
prepare_Rd: planarFaceTraversal.Rd:19-20: Dropping empty section \value
prepare_Rd: removeSelfLoops.Rd:27: Dropping empty section \seealso
prepare_Rd: sloanStartEndVertices.Rd:16-17: Dropping empty section \details
prepare_Rd: sloanStartEndVertices.Rd:19-20: Dropping empty section \value
prepare_Rd: sloanStartEndVertices.Rd:33-34: Dropping empty section \examples
prepare_Rd: transClosure.Rd:36: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... 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

RBGL.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'RBGL' ...
found boostIncl header sources and tar archive;\n using what is there.
** libs
  making DLL ...
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c bbc.cpp -o bbc.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from bbc.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
In file included from boostIncl/boost/graph/dijkstra_shortest_paths.hpp:15,
                 from boostIncl/boost/graph/betweenness_centrality.hpp:14,
                 from bbc.cpp:2:
boostIncl/boost/utility/compare_pointees.hpp: In function 'void boost::breadth_first_visit(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, Buffer&, BFSVisitor, ColorMap) [with IncidenceGraph = 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>, Buffer = boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<Graph>::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 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 long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::allocator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, 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 long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long 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 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 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 long unsigned int>, double, double&>, WeightMap = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long 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 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 long unsigned int>, boost::default_color_type, boost::default_color_type&>]::MutableQueue, BFSVisitor = 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 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 long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::allocator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, 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 long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long 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 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 long unsigned int>, long long unsigned int, long long unsigned int&> >, boost::relaxed_heap<long 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 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 long unsigned int> >, boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long 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 long unsigned int>, double, double&>, boost::closed_plus<double>, std::less<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 long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
In file included from bbc.cpp:2:
boostIncl/boost/optional/optional.hpp: In function 'void boost::detail::graph::brandes_betweenness_centrality_impl(const Graph&, CentralityMap, EdgeCentralityMap, IncomingMap, DistanceMap, DependencyMap, PathCountMap, VertexIndexMap, ShortestPaths) [with Graph = 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>, CentralityMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_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::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>*, double, double&, boost::vertex_centrality_t>, EdgeCentralityMap = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::edge_centrality_t>, IncomingMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::allocator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, 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 long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >&>, 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 long unsigned int>, double, double&>, DependencyMap = 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 long unsigned int>, double, double&>, PathCountMap = 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 long unsigned int>, long long unsigned int, long long unsigned int&>, VertexIndexMap = 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 long unsigned int>, ShortestPaths = boost::detail::graph::brandes_dijkstra_shortest_paths<boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::edge_weight_t> >]':
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c cliques.cpp -o cliques.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from cliques.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c clusteringCoef.cpp -o clusteringCoef.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from clusteringCoef.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c dominatorTree.cpp -o dominatorTree.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from dominatorTree.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from edmonds_optimum_branching.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c hcs.cpp -o hcs.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from hcs.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c incrConnComp.cpp -o incrConnComp.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from incrConnComp.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c interfaces.cpp -o interfaces.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from interfaces.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c layout.cpp -o layout.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from layout.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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'
In file included from layout.cpp:9:
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 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
In file included from boostIncl/boost/graph/dijkstra_shortest_paths.hpp:15,
                 from boostIncl/boost/graph/johnson_all_pairs_shortest.hpp:28,
                 from boostIncl/boost/graph/kamada_kawai_spring_layout.hpp:13,
                 from layout.cpp:3:
boostIncl/boost/utility/compare_pointees.hpp: In function 'void boost::breadth_first_visit(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, Buffer&, BFSVisitor, ColorMap) [with IncidenceGraph = 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>, Buffer = boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<Graph>::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 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 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 long unsigned int>, boost::default_color_type, boost::default_color_type&>]::MutableQueue, BFSVisitor = boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long 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 long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long 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> >, 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 long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
In file included from boostIncl/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from boostIncl/boost/graph/kamada_kawai_spring_layout.hpp:13,
                 from layout.cpp:3:
boostIncl/boost/optional/optional.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, 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 long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, BinaryPredicate = std::less<double>, BinaryFunction = boost::closed_plus<double>, Infinity = double, DistanceZero = double]::Graph2, Size = long long unsigned int, WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight_t>, 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>, BinaryFunction = boost::closed_plus<double>, BinaryPredicate = std::less<double>, BellmanFordVisitor = boost::bellman_visitor<boost::null_visitor>]':
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c minST.cpp -o minST.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from minST.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
In file included from minST.cpp:2:
boostIncl/boost/optional/optional.hpp: In function 'void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list<boost::directedS, double>, OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int> > > >, Rank = 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_color_t, boost::default_color_type, boost::no_property>, long long unsigned int>, long long unsigned int, long long unsigned int&>, Parent = 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_color_t, boost::default_color_type, boost::no_property>, long long unsigned int>, long long unsigned int, long long unsigned int&>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>]':
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp: In function 'SEXPREC* BGL_PRIM_U(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c mincut.cpp -o mincut.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from mincut.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c ordering.cpp -o ordering.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from ordering.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c planar.cpp -o planar.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from planar.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
planar.cpp: In function 'SEXPREC* planarFaceTraversal(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:151: warning: comparison between signed and unsigned integer expressions
planar.cpp:153: warning: comparison between signed and unsigned integer expressions
planar.cpp:161: warning: comparison between signed and unsigned integer expressions
planar.cpp:165: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function 'SEXPREC* planarCanonicalOrdering(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:256: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function 'SEXPREC* isStraightLineDrawing(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:369: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function 'SEXPREC* isKuratowskiSubgraph(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:461: warning: unused variable 'i'
planar.cpp: In function 'SEXPREC* makeConnected(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:485: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function 'SEXPREC* makeBiconnectedPlanar(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:539: warning: comparison between signed and unsigned integer expressions
In file included from planar.cpp:11:
boostIncl/boost/graph/max_cardinality_matching.hpp: In member function 'bool boost::edmonds_augmenting_path_finder<Graph, MateMap, VertexIndexMap>::augment_matching() [with Graph = R_adjacency_list<boost::undirectedS, int>, MateMap = long 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 long unsigned int>]':
boostIncl/boost/graph/max_cardinality_matching.hpp:231: warning: 'v' may be used uninitialized in this function
boostIncl/boost/graph/max_cardinality_matching.hpp:231: warning: 'w' may be used uninitialized in this function
In file included from boostIncl/boost/graph/boyer_myrvold_planar_test.hpp:12,
                 from planar.cpp:3:
boostIncl/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function 'void boost::boyer_myrvold_impl<Graph, VertexIndexMap, StoreOldHandlesPolicy, StoreEmbeddingPolicy>::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > > >, EdgeIndexMap = boost::adj_list_edge_property_map<boost::undirected_tag, int, int&, long long unsigned int, boost::property<boost::edge_index_t, int, boost::no_property>, boost::edge_index_t>, Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS>, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, long long unsigned int>, StoreOldHandlesPolicy = boost::graph::detail::store_old_handles, StoreEmbeddingPolicy = boost::graph::detail::no_embedding]':
boostIncl/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1279: warning: 'previous_vertex' may be used uninitialized in this function
boostIncl/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1238: warning: 'bicomp_root' may be used uninitialized in this function
boostIncl/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1237: warning: 'z' may be used uninitialized in this function
In file included from planar.cpp:5:
boostIncl/boost/graph/planar_canonical_ordering.hpp: In function 'void boost::planar_canonical_ordering(const Graph&, PlanarEmbedding, OutputIterator, VertexIndexMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS>, PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::allocator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > > > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, long long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >&>, OutputIterator = std::back_insert_iterator<std::vector<long long unsigned int, std::allocator<long long unsigned int> > >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, long long unsigned int>]':
boostIncl/boost/graph/planar_canonical_ordering.hpp:68: warning: 'second_vertex' may be used uninitialized in this function
In file included from planar.cpp:6:
boostIncl/boost/graph/chrobak_payne_drawing.hpp: In function 'void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, VertexIndexMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS>, PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::allocator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > > > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, long long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int>, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > >&>, ForwardIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int, std::allocator<long long unsigned int> > >, GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<coord_t*, std::vector<coord_t, std::allocator<coord_t> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, long long unsigned int>, coord_t, coord_t&>, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, long long unsigned int>]':
boostIncl/boost/graph/chrobak_payne_drawing.hpp:208: warning: 'next_to_rightmost' may be used uninitialized in this function
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c shortestPath.cpp -o shortestPath.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from shortestPath.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
In file included from boostIncl/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from shortestPath.cpp:4:
boostIncl/boost/optional/optional.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::no_property, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>, Size = int, WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, PredecessorMap = long long unsigned int*, DistanceMap = double*, BinaryFunction = boost::closed_plus<double>, BinaryPredicate = std::less<double>, BellmanFordVisitor = boost::bellman_visitor<boost::null_visitor>]':
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
In file included from boostIncl/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from shortestPath.cpp:4:
boostIncl/boost/optional/optional.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, 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 long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, BinaryPredicate = std::less<double>, BinaryFunction = boost::closed_plus<double>, Infinity = double, DistanceZero = double]::Graph2, Size = long long unsigned int, WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight_t>, 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>, BinaryFunction = boost::closed_plus<double>, BinaryPredicate = std::less<double>, BellmanFordVisitor = boost::bellman_visitor<boost::null_visitor>]':
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
In file included from boostIncl/boost/graph/dijkstra_shortest_paths.hpp:15,
                 from shortestPath.cpp:3:
boostIncl/boost/utility/compare_pointees.hpp: In function 'void boost::breadth_first_visit(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, Buffer&, BFSVisitor, ColorMap) [with IncidenceGraph = R_adjacency_list<boost::directedS, double>, Buffer = boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, PredecessorMap, DistanceMap, WeightMap, IndexMap, Compare, Combine, DistZero, DijkstraVisitor, ColorMap) [with VertexListGraph = R_adjacency_list<boost::directedS, double>, DijkstraVisitor = boost::dijkstra_visitor<boost::null_visitor>, PredecessorMap = long long unsigned int*, DistanceMap = double*, WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, IndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long 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_color_t, boost::default_color_type, boost::no_property>, long long unsigned int>, boost::default_color_type, boost::default_color_type&>]::MutableQueue, BFSVisitor = boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long long unsigned int, boost::indirect_cmp<double*, std::less<double> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, long long unsigned int*, double*, boost::closed_plus<double>, std::less<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_color_t, boost::default_color_type, boost::no_property>, long long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/utility/compare_pointees.hpp: In function 'void boost::breadth_first_visit(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, Buffer&, BFSVisitor, ColorMap) [with IncidenceGraph = 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>, Buffer = boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<Graph>::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 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 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 long unsigned int>, boost::default_color_type, boost::default_color_type&>]::MutableQueue, BFSVisitor = boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long 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 long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long 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> >, 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 long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp: In function 'SEXPREC* BGL_dijkstra_shortest_paths_D(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c sna.cpp -o sna.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from sna.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
In file included from boostIncl/boost/graph/adjacency_list.hpp:313,
                 from RBGL.hpp:26,
                 from sna.cpp:1:
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::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 long unsigned int>, boost::no_property> > >, boost::no_property, boost::listS>, Config = boost::detail::adj_list_gen<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 long unsigned int>, boost::no_property> > >, boost::no_property, boost::listS>, 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 long unsigned int>, 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::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 long unsigned int>, boost::no_property> > >, boost::no_property, boost::listS>, 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 long unsigned int>, boost::no_property> > >, boost::no_property, boost::listS>::config>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:270: warning: 'p.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 long unsigned int>, boost::no_property> > >::<anonymous>.boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, boost::no_property> >::<anonymous>.boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, boost::no_property>::m_value.boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>::<anonymous>.boost::detail::edge_base<boost::directed_tag, long long unsigned int>::m_target' may be used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:2232: note: 'p.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 long unsigned int>, boost::no_property> > >::<anonymous>.boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, boost::no_property> >::<anonymous>.boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, boost::no_property>::m_value.boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>::<anonymous>.boost::detail::edge_base<boost::directed_tag, long long unsigned int>::m_target' was declared here
boostIncl/boost/graph/detail/adjacency_list.hpp:270: warning: 'p.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 long unsigned int>, boost::no_property> > >::<anonymous>.boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, boost::no_property> >::<anonymous>.boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, boost::no_property>::m_value.boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>::<anonymous>.boost::detail::edge_base<boost::directed_tag, long long unsigned int>::m_source' may be used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:2232: note: 'p.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 long unsigned int>, boost::no_property> > >::<anonymous>.boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, boost::no_property> >::<anonymous>.boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, boost::no_property>::m_value.boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>::<anonymous>.boost::detail::edge_base<boost::directed_tag, long long unsigned int>::m_source' was declared here
In file included from boostIncl/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from sna.cpp:3:
boostIncl/boost/optional/optional.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, 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 long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, BinaryPredicate = std::less<double>, BinaryFunction = boost::closed_plus<double>, Infinity = double, DistanceZero = double]::Graph2, Size = long long unsigned int, WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight_t>, 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>, BinaryFunction = boost::closed_plus<double>, BinaryPredicate = std::less<double>, BellmanFordVisitor = boost::bellman_visitor<boost::null_visitor>]':
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:262: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:268: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
In file included from boostIncl/boost/graph/dijkstra_shortest_paths.hpp:15,
                 from boostIncl/boost/graph/johnson_all_pairs_shortest.hpp:28,
                 from sna.cpp:3:
boostIncl/boost/utility/compare_pointees.hpp: In function 'void boost::breadth_first_visit(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, Buffer&, BFSVisitor, ColorMap) [with IncidenceGraph = 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>, Buffer = boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits<Graph>::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 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 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 long unsigned int>, boost::default_color_type, boost::default_color_type&>]::MutableQueue, BFSVisitor = boost::detail::dijkstra_bfs_visitor<boost::dijkstra_visitor<boost::null_visitor>, boost::relaxed_heap<long 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 long unsigned int> >, boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long 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> >, 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 long unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
boostIncl/boost/utility/compare_pointees.hpp:32: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c transitive_closure.cpp -o transitive_closure.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from transitive_closure.cpp:16:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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/optional/optional.hpp: In function 'SEXPREC* BGL_transitive_closure_D(SEXPREC*, SEXPREC*, SEXPREC*)':
boostIncl/boost/optional/optional.hpp:315: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
boostIncl/boost/optional/optional.hpp:422: note: initialized from here
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"      -IboostIncl    -O2 -Wall  -c wavefront.cpp -o wavefront.o
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/hash_set:60,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from wavefront.cpp:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.4.4/backward/backward_warning.h:28:2: 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.
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o RBGL.dll tmp.def bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o layout.o minST.o mincut.o ordering.o planar.o shortestPath.o sna.o transitive_closure.o wavefront.o -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/RBGL.Rcheck/RBGL/libs/x64
  ... done
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RBGL)

RBGL.Rcheck/RBGL-Ex.timings:

nameusersystemelapsed
FileDep0.780.030.82
astarSearch0.060.000.06
bandwidth0.030.000.03
bccluster0.020.000.06
bellman.ford.sp0.020.000.01
betweenness0.010.000.02
bfs0.040.000.03
biConnComp0.010.000.02
chrobakPayneStraightLineDrawing0.030.000.03
clusteringCoef0.020.000.01
clusteringCoefAppr0.010.000.02
coloring0.000.020.01
connectedComp0.040.000.07
dag.sp0.010.000.01
dijkstra.sp0.050.000.05
dominatorTree0.000.010.01
edgeConn0.010.000.02
edmondsMaxCardinalityMatching0.030.000.03
edmondsOptimumBranching0.020.000.02
extractPath000
floyd.warshall.all.pairs.sp0.020.000.02
gprofile0.010.000.01
graphGenerator000
highlyConnSG0.020.000.02
incrConnComp0.010.000.02
is.triangulated0.020.010.03
isKuratowskiSubgraph0.030.000.03
isStraightLineDrawing0.020.000.01
isomorphism0.030.000.03
johnson.all.pairs.sp0.010.000.02
kCliques0.020.000.02
kCores0.090.000.09
lambdaSets0.020.000.02
layout0.090.000.09
makeBiconnectedPlanar0.030.000.03
makeConnected0.020.000.02
makeMaximalPlanar0.010.000.01
maxClique0.000.020.01
maxFlow0.020.010.03
minCut0.010.000.02
mstree.kruskal0.050.000.05
mstree.prim0.020.000.01
ordering0.010.000.02
planarCanonicalOrdering0.020.000.01
planarFaceTraversal0.010.000.02
removeSelfLoops0.020.000.02
separates0.030.000.03
sp.between0.050.000.05
strongComp0.030.000.03
transClosure0.010.000.02
transitivity0.020.000.01
tsort0.020.000.02
wavefront0.010.000.01