deprecated head file for RBGL and compilation failure
1
0
Entering edit mode
Guest User ★ 13k
@guest-user-4897
Last seen 9.6 years ago
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.
graph RBGL PROcess graph RBGL PROcess • 1.5k views
ADD COMMENT
0
Entering edit mode
@vincent-j-carey-jr-4
Last seen 16 days ago
United States
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 COMMENT

Login before adding your answer.

Traffic: 586 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6