Question: deprecated head file for RBGL and compilation failure
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Guest User12k
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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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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/bac kward/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::Incide nceGraphConcept<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::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::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_proper ty_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::v ector<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_vis itor<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::prope rty<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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ADD COMMENTlink modified 7.5 years ago by Vincent J. Carey, Jr.6.3k • written 7.5 years ago by Guest User12k
Answer: deprecated head file for RBGL and compilation failure
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gravatar for Vincent J. Carey, Jr.
7.5 years ago by
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Vincent J. Carey, Jr.6.3k wrote:
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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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/b ackward/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::~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<unsig ned=""> 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<unsig ned=""> 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<unsig ned=""> int> > >; ColorMap = > boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::def ault_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<unsig ned=""> int> > >; ColorMap = > boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::def ault_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<unsig ned=""> int> > >; P = > boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsig ned=""> 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<unsig ned=""> 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_colo r_t,=""> boost::default_color_type>, unsigned int>, unsigned int, unsigned int&>; > VertexIndexMap = > boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_colo r_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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.5 years ago by Vincent J. Carey, Jr.6.3k
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