Thanks for this report.  I did not encounter these warnings/errors with
earlier gcc -- for example, the install is
perfectly clean with

rex-bash-3.2$ gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada
--enable-java-awt=gtk --disable-dssi --enable-plugin
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic
--host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)

However, the central build system with gcc 4.6 does report warnings in
compiilation and these will be attended to.  I would like to see us do a
better job of clarifying which version of boost source is being used.  With
the current svn checkout of boost-trunk, I find that adding

-std=gnu++0x -DBOOST_NO_HASH

to the Makevars gets us more mileage, but more work is needed.  Tested
patches are of course welcome.

On Sun, Apr 15, 2012 at 4:05 AM, eastasiax [guest]
<guest@bioconductor.org>wrote:

>
> please update qt header file to version 4.8 or greater. there were many
> warnings while compiling. here are some:
> * installing *source* package ‘RBGL’ ...
> untarring boost include tree...
> ** libs
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c bbc.cpp -o bbc.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from bbc.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c cliques.cpp -o cliques.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from cliques.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c clusteringCoef.cpp -o
> clusteringCoef.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from clusteringCoef.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c dominatorTree.cpp -o
> dominatorTree.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from dominatorTree.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c
> edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from edmonds_optimum_branching.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c hcs.cpp -o hcs.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from hcs.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c incrConnComp.cpp -o
> incrConnComp.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from incrConnComp.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c interfaces.cpp -o
> interfaces.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from interfaces.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c layout.cpp -o layout.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from layout.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c minST.cpp -o minST.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from minST.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c mincut.cpp -o mincut.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from mincut.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c ordering.cpp -o ordering.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from ordering.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c planar.cpp -o planar.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from planar.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c shortestPath.cpp -o
> shortestPath.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from shortestPath.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c sna.cpp -o sna.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from sna.cpp:1:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
> g++ -I/usr/include/R/ -DNDEBUG  -I/usr/local/include   -IboostIncl  -fpic
>  -march=i686 -mtune=generic -O2 -pipe -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -c transitive_closure.cpp -o
> transitive_closure.o
> In file included from
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:25,
>                 from RBGL.hpp:26,
>                 from transitive_closure.cpp:16:
> /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
>
> some errors caused interrupt of compilation process.
>
> In file included from boostIncl/boost/graph/detail/adjacency_list.hpp:30:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:313,
>                 from RBGL.hpp:26,
>                 from transitive_closure.cpp:16:
> boostIncl/boost/graph/graph_concepts.hpp: In instantiation of
> ‘boost::concepts::IncidenceGraph<G>::~IncidenceGraph() [with G =
> std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned
> int> > >]’:
> boostIncl/boost/graph/graph_concepts.hpp:70:1:   required from ‘static
> void boost::concept::requirement<Model>::failed() [with Model =
> boost::concepts::IncidenceGraphConcept<std::vector<std::vector<unsigned
> int>, std::allocator<std::vector<unsigned int> > > >]’
> boostIncl/boost/concept_check.hpp:43:1:   required from ‘void
> boost::function_requires(Model*) [with Model =
> boost::concepts::IncidenceGraphConcept<std::vector<std::vector<unsigned
> int>, std::allocator<std::vector<unsigned int> > > >]’
> boostIncl/boost/graph/depth_first_search.hpp:84:7:   required from ‘void
> boost::detail::depth_first_visit_impl(const IncidenceGraph&, typename
> boost::graph_traits<Graph>::vertex_descriptor, DFSVisitor&, ColorMap,
> TerminatorFunc) [with IncidenceGraph = std::vector<std::vector<unsigned
> int>, std::allocator<std::vector<unsigned int> > >; DFSVisitor =
> boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned
> int> > >; ColorMap =
> boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::default_color_type*,
> std::vector<boost::default_color_type> >, boost::identity_property_map,
> boost::default_color_type, boost::default_color_type&>; TerminatorFunc =
> boost::detail::nontruth2; typename
> boost::graph_traits<Graph>::vertex_descriptor = unsigned int]’
> boostIncl/boost/graph/depth_first_search.hpp:201:7:   required from
> ‘void boost::depth_first_search(const VertexListGraph&, DFSVisitor,
> ColorMap, typename boost::graph_traits<Graph>::vertex_descriptor) [with
> VertexListGraph = std::vector<std::vector<unsigned int>,
> std::allocator<std::vector<unsigned int> > >; DFSVisitor =
> boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned
> int> > >; ColorMap =
> boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::default_color_type*,
> std::vector<boost::default_color_type> >, boost::identity_property_map,
> boost::default_color_type, boost::default_color_type&>; typename
> boost::graph_traits<Graph>::vertex_descriptor = unsigned int]’
> boostIncl/boost/graph/depth_first_search.hpp:249:9:   required from
> ‘static void
> boost::detail::dfs_dispatch<boost::detail::error_property_not_found>::apply(const
> VertexListGraph&, DFSVisitor, Vertex, const boost::bgl_named_params<P, T,
> R>&, boost::detail::error_property_not_found) [with VertexListGraph =
> std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned
> int> > >; Vertex = unsigned int; DFSVisitor =
> boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned
> int> > >; P =
> boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned
> int> > >; T = boost::graph_visitor_t; R =
> boost::bgl_named_params<boost::identity_property_map,
> boost::vertex_index_t, boost::no_property>]’
> boostIncl/boost/graph/depth_first_search.hpp:329:5:   required from
> ‘void boost::depth_first_search(const VertexListGraph&, const
> boost::bgl_named_params<P, T, R>&) [with VertexListGraph =
> std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned
> int> > >; P =
> boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned
> int> > >; T = boost::graph_visitor_t; R =
> boost::bgl_named_params<boost::identity_property_map,
> boost::vertex_index_t, boost::no_property>]’
> boostIncl/boost/graph/topological_sort.hpp:64:5:   required from ‘void
> boost::topological_sort(VertexListGraph&, OutputIterator, const
> boost::bgl_named_params<P, T, R>&) [with VertexListGraph =
> std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned
> int> > >; OutputIterator = std::back_insert_iterator<std::vector<unsigned
> int> >; P = boost::identity_property_map; T = boost::vertex_index_t; R =
> boost::no_property]’
> boostIncl/boost/graph/transitive_closure.hpp:120:5:   required from
> ‘void boost::transitive_closure(const Graph&, GraphTC&,
> G_to_TC_VertexMap, VertexIndexMap) [with Graph =
> R_adjacency_list<boost::directedS, double>; GraphTC =
> R_adjacency_list<boost::directedS, double>; G_to_TC_VertexMap =
> boost::iterator_property_map<unsigned int*,
> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t,
> boost::default_color_type>, unsigned int>, unsigned int, unsigned int&>;
> VertexIndexMap =
> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t,
> boost::default_color_type>, unsigned int>]’
> boostIncl/boost/graph/transitive_closure.hpp:263:5:   required from
> ‘void boost::transitive_closure(const Graph&, GraphTC&) [with Graph =
> R_adjacency_list<boost::directedS, double>; GraphTC =
> R_adjacency_list<boost::directedS, double>]’
> transitive_closure.cpp:29:30:   required from here
> boostIncl/boost/graph/graph_concepts.hpp:88:11: error: ‘out_edges’ was
> not declared in this scope, and no declarations were found by
> argument-dependent lookup at the point of instantiation [-fpermissive]
> In file included from boostIncl/boost/graph/transpose_graph.hpp:16:0,
>                 from boostIncl/boost/graph/strong_components.hpp:258,
>                 from boostIncl/boost/graph/transitive_closure.hpp:18,
>                 from transitive_closure.cpp:17:
> boostIncl/boost/graph/reverse_graph.hpp:151:1: note: ‘template<class
> BidirectionalGraph, class GRef> std::pair<typename
> boost::graph_traits<Graph>::in_edge_iterator, typename
> boost::graph_traits<Graph>::in_edge_iterator> boost::out_edges(typename
> boost::graph_traits<Graph>::vertex_descriptor, const
> boost::reverse_graph<Graph, GraphRef>&)’ declared here, later in the
> translation unit
> In file included from boostIncl/boost/graph/detail/adjacency_list.hpp:30:0,
>                 from boostIncl/boost/graph/adjacency_list.hpp:313,
>                 from RBGL.hpp:26,
>                 from transitive_closure.cpp:16:
> boostIncl/boost/graph/graph_concepts.hpp:89:11: error: ‘out_degree’
> was not declared in this scope, and no declarations were found by
> argument-dependent lookup at the point of instantiation [-fpermissive]
> In file included from boostIncl/boost/graph/transpose_graph.hpp:16:0,
>                 from boostIncl/boost/graph/strong_components.hpp:258,
>                 from boostIncl/boost/graph/transitive_closure.hpp:18,
>                 from transitive_closure.cpp:17:
> boostIncl/boost/graph/reverse_graph.hpp:173:1: note: ‘template<class
> BidirectionalGraph, class GRef> typename
> boost::graph_traits<Graph>::degree_size_type boost::out_degree(typename
> boost::graph_traits<Graph>::vertex_descriptor, const
> boost::reverse_graph<Graph, GraphRef>&)’ declared here, later in the
> translation unit
> make: *** [transitive_closure.o] Error 1
> ERROR: compilation failed for package ‘RBGL’
> * removing ‘/home/neoanima/.Rlib/RBGL’
>
> The downloaded source packages are in
>        ‘/tmp/RtmpOs7NUf/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>  installation of package ‘RBGL’ had non-zero exit status
>
> please fix them.
>
>  -- output of sessionInfo():
>
> R>sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>  [1] LC_CTYPE=zh_CN.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=C
>  [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=C                LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] BiocInstaller_1.4.3 MASS_7.3-17
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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>

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