hi, i'm just moving from R 2.2 and BioC 1.7 to R 2.3 and BioC 1.8, but got a problem when i tried to install the RBGL package. i included the whole output of the R CMD INSTALL call in the attachment, below is just the error message that causes the installation failure: boostIncl/boost/graph/depth_first_search.hpp:324: error: no matching function for call to 'vertices(const std::vector<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> >, std::allocator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > > >&)' make: *** [interfaces.o] Error 1 chmod: cannot access `/usr/lib64/R/library/RBGL/libs/*': No such file or directory ERROR: compilation failed for package 'RBGL' ** Removing '/usr/lib64/R/library/RBGL' i don't know if that is a problem of my system (running fedora core 5 on a amd64) or not. has anyone experienced the same problems, or has anyone a solution to this problem? thanks in advance, jo -- Johannes Rainer, Msc Tyrolean Cancer Research Institute Innrain 66, 6020 Innsbruck, Austria Tel.: +43 512 570485 15 Email: johannes.rainer at tcri.at johannes.rainer at tugraz.at -------------- next part -------------- R CMD INSTALL RBGL_1.8.1.tar.gz * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c bbc.cpp -o bbc.o boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'void boost::detail::dijkstra_dispatch2(const VertexListGraph&, typename boost::graph_traits<g>::vertex_descriptor, DistanceMap, WeightMap, IndexMap, const Params&) [with VertexListGraph = boost::adjacency_list<boost::vecs, boost::vecs,="" boost::undirecteds,="" boost::property<boost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, boost::property<boost::edge_weight_t, double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::no_property, boost::listS>, DistanceMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, boost::vec_adj_list_ve rtex_id_map<boost::property<boost::vertex_index_t, int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, double, double&>, WeightMap = boost::adj_list_edge_property_map<boost::undirected_tag, double,="" double&,="" long="" unsigned="" int,="" boost::property<boost::edge_weight_t,="" double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::edge_weight_t>, IndexMap = boost::vec_ad j_list_vertex_id_map<boost::property<boost::vertex_index_t, int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, Params = boost::bgl_named_p arams<boost::detail::graph::brandes_dijkstra_visitor<const boost::adjacency_list<boost::vecs,="" boost::vecs,="" boost::undirecteds,="" boost::property<boost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, boost::property<boost::edge_weight_t, double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::no_property, boost::listS>, boost::adj_list_edge_property_map<boost::undirected_tag, double,="" double&,="" long="" unsigned="" int,="" boost::property<boost::edge_weight_t,="" double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::edge_weight_t>, boost::iterator_property _map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc _impl<boost::undirected_tag,="" long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > >*, std::vector<std::vector<boost::detail::edge_d esc_impl<boost::undirected_tag,="" long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > >, std::allocator<std::vector<boost::detail::edge _desc_impl<boost::undirected_tag,="" long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > > > > >, boost::vec_adj_list_vertex_id_map<boost: :property<boost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > >, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > >&>, boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, boost::vec_adj_list_ve rtex_id_map<boost::property<boost::vertex_index_t, int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, double, double&>, boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned="" int*,="" std::vector<long="" unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > >, boost::vec_adj_list_vertex_id_map<boost::property<b oost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, long unsigned int, long unsigned int&> >, boost::graph_visitor_t, boost::bgl_named_params <boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, boost::vec_adj_list_ve rtex_id_map<boost::property<boost::vertex_index_t, int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, double, double&>, boost::vertex_distance_t, boost::bgl_named_params<boost::vec_adj_list_ vertex_id_map<boost::property<boost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, boost::vertex_index_t, boos t::bgl_named_params<boost::adj_list_edge_property_map<boost::undirecte d_tag,="" double,="" double&,="" long="" unsigned="" int,="" boost::property<boost::edge_weight_t,="" double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::edge_weight_t>, boost::edge_weight_t, boost::no_property> > > >]': boostIncl/boost/graph/dijkstra_shortest_paths.hpp:95: warning: 'bfs_vis$m_decreased' is used uninitialized in this function g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c cliques.cpp -o cliques.o cliques.cpp: In function 'void print_one_clique(oneCliqueType&)': cliques.cpp:110: warning: comparison between signed and unsigned integer expressions cliques.cpp: In function 'void print_all_cliques(allCliquesType&, char*)': cliques.cpp:118: warning: comparison between signed and unsigned integer expressions cliques.cpp: In function 'void extend_v2(Graph_ud&, std::vector<int, std::allocator<int=""> >&, std::vector<int, std::allocator<int=""> >&, int, int, int&, allCliquesType&)': cliques.cpp:139: warning: 's' may be used uninitialized in this function cliques.cpp:139: warning: 'pos' may be used uninitialized in this function cliques.cpp:138: warning: 'fixp' may be used uninitialized in this function cliques.cpp: At global scope: cliques.cpp:115: warning: 'void print_all_cliques(allCliquesType&, char*)' defined but not used g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c hcs.cpp -o hcs.o hcs.cpp: In function 'void output_graph_labels(const V_Label&, const char*)': hcs.cpp:27: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void build_subgraph(Cluster&, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)': hcs.cpp:62: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void remove_vertices(int, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)': hcs.cpp:117: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'dst cluster_distance(const Graph_ud&, V_Label&, int, V_Label&)': hcs.cpp:134: warning: comparison between signed and unsigned integer expressions hcs.cpp:138: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void adopt_singleton(const Graph_ud&, V_Label&, ClusterResult&)': hcs.cpp:206: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void remove_clusters(ClusterResult&, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)': hcs.cpp:248: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void HCS_internal(const Graph_ud&, V_Label&, ClusterResult&)': hcs.cpp:288: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'SEXPREC* HCS_loop(Graph_ud&, V_Label&)': hcs.cpp:363: warning: comparison between signed and unsigned integer expressions hcs.cpp:393: warning: comparison between signed and unsigned integer expressions hcs.cpp:397: warning: comparison between signed and unsigned integer expressions hcs.cpp:353: warning: unused variable 'found_new_cluster' boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'typename boost::graph_traits<g>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list<boost::undirecteds, double="">, OutputIterator = std::back_insert_iterator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > >]': boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$m_value' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$m_value' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$D108232$m_value$D106029$m_target' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$D108232$m_value$D106029$m_source' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$m_value' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$m_value' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$D108232$m_value$D106029$m_target' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$D108232$m_value$D106029$m_source' is used uninitialized in this function boostIncl/boost/graph/edge_connectivity.hpp:32: warning: 'p' may be used uninitialized in this function hcs.cpp: At global scope: hcs.cpp:24: warning: 'void output_graph_labels(const V_Label&, const char*)' defined but not used hcs.cpp:32: warning: 'void output_graph(const Graph_ud&, const char*)' defined but not used g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c incrConnComp.cpp -o incrConnComp.o incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXPREC*, SEXPREC*, SEXPREC*, E_IC_METHOD)': incrConnComp.cpp:67: warning: comparison between signed and unsigned integer expressions g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c interfaces.cpp -o interfaces.o interfaces.cpp: In function 'SEXPREC* BGL_articulation_points_U(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)': interfaces.cpp:311: warning: comparison between signed and unsigned integer expressions boostIncl/boost/graph/depth_first_search.hpp: In function 'void boost::depth_first_search(const VertexListGraph&, const boost::bgl_named_params<p, t,="" r="">&) [with VertexListGraph = std::vector<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> >, std::allocator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > > >, P = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<long unsigned="" int,="" std::allocator<long="" 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: instantiated from 'void boost::topological_sort(VertexListGraph&, OutputIterator, const boost::bgl_named_params<p, t,="" r="">&) [with VertexListGraph = std::vector<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> >, std::allocator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > > >, OutputIterator = std::back_insert_iterator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > >, P = boost::identity_property_map, T = boost::vertex_index_t, R = boost::no_property]' boostIncl/boost/graph/transitive_closure.hpp:120: instantiated 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<bgl_sequential_vertex_coloring::vertex_size_typ e*,="" boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_co="" lor_t,="" boost::default_color_type,="" boost::no_property="">, long unsigned int>, long unsigned int, long unsigned int&>, VertexIndexMap = boost:: vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type,="" boost::no_property="">, long unsigned int>]' boostIncl/boost/graph/transitive_closure.hpp:263: instantiated from 'void boost::transitive_closure(const Graph&, GraphTC&) [with Graph = Graph_dd, GraphTC = Graph_dd]' interfaces.cpp:371: instantiated from here boostIncl/boost/graph/depth_first_search.hpp:324: error: no matching function for call to 'vertices(const std::vector<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> >, std::allocator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > > >&)' make: *** [interfaces.o] Error 1 chmod: cannot access `/usr/lib64/R/library/RBGL/libs/*': No such file or directory ERROR: compilation failed for package 'RBGL' ** Removing '/usr/lib64/R/library/RBGL'

hi Li thanks for your quick reply, concerning the extra parameters, i have not defined anything, i just downloaded the RBGL_1.8.1.tar.gz and run R CMD INSTALL on it, i did not specify any extra parameter... don't know from where they are coming. actually the R i installed is a precompiled one, i got it from one of the fedora repositories, before i installed this one i compiled it myself, but was also not able to install RBGL. R CMD INSTALL --configure-args='-g -O2' RBGL_1.8.1.tar.gz also resulted in an error (see the attachment). the version of g++ (i suppose it is an x86_64 version, at least it supports m32 and m64...): [jo at bugblatterbeast ~]$ g++ --version g++ (GCC) 4.1.0 20060304 (Red Hat 4.1.0-3) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. i will now try to install it on an other machine running FC5, perhaps there is something wrong with my system... thanks jo On 5/11/06, Li.Long at isb-sib.ch <li.long at="" isb-sib.ch=""> wrote: > > > Hi, > > I'll be really interested in finding out what's happening in your > settings. > Could you provide additional info > o. why/how did you decide to use the extra parameters when compiling? > (such as protect-stack, and the like) If you just use "-g -O2", what do > you get? > o. what version of g++ do you have? is it for 64bit? > > It's my package, I'll try to help you figure it out. > > Thanks > > Li > > > hi, > > i'm just moving from R 2.2 and BioC 1.7 to R 2.3 and BioC 1.8, but got a > > problem when i tried to install the RBGL package. i included the whole > > output of the R CMD INSTALL call in the attachment, below is just the > > error > > message that causes the installation failure: > > > > > > boostIncl/boost/graph/depth_first_search.hpp:324: error: no matching > > function for call to 'vertices(const std::vector<std::vector<long> unsigned > > int, std::allocator<long unsigned="" int=""> >, > std::allocator<std::vector<long> > unsigned int, std::allocator<long unsigned="" int=""> > > >&)' > > make: *** [interfaces.o] Error 1 > > chmod: cannot access `/usr/lib64/R/library/RBGL/libs/*': No such file or > > directory > > ERROR: compilation failed for package 'RBGL' > > ** Removing '/usr/lib64/R/library/RBGL' > > > > i don't know if that is a problem of my system (running fedora core 5 on > a > > amd64) or not. has anyone experienced the same problems, or has anyone a > > solution to this problem? > > > > thanks in advance, > > jo > > -- > > Johannes Rainer, Msc > > Tyrolean Cancer Research Institute > > Innrain 66, 6020 Innsbruck, Austria > > Tel.: +43 512 570485 15 > > Email: johannes.rainer at tcri.at > > johannes.rainer at tugraz.at > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Johannes Rainer, Msc Tyrolean Cancer Research Institute Innrain 66, 6020 Innsbruck, Austria Tel.: +43 512 570485 15 Email: johannes.rainer at tcri.at johannes.rainer at tugraz.at -------------- next part -------------- R CMD INSTALL --configure-args='-g -O2' RBGL_1.8.1.tar.gz * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c bbc.cpp -o bbc.o boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'void boost::detail::dijkstra_dispatch2(const VertexListGraph&, typename boost::graph_traits::vertex_descriptor, DistanceMap, WeightMap, IndexMap, const Params&) [with VertexListGraph = boost::adjacency_list<boost::vecs, boost::vecs,="" boost::undirecteds,="" boost::property<boost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, boost::property<boost::edge_weight_t, double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::no_property, boost::listS>, DistanceMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, boost::vec_adj_list_ve rtex_id_map<boost::property<boost::vertex_index_t, int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, double, double&>, WeightMap = boost::adj_list_edge_property_map<boost::undirected_tag, double,="" double&,="" long="" unsigned="" int,="" boost::property<boost::edge_weight_t,="" double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::edge_weight_t>, IndexMap = boost::vec_ad j_list_vertex_id_map<boost::property<boost::vertex_index_t, int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, Params = boost::bgl_named_p arams<boost::detail::graph::brandes_dijkstra_visitor<const boost::adjacency_list<boost::vecs,="" boost::vecs,="" boost::undirecteds,="" boost::property<boost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, boost::property<boost::edge_weight_t, double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::no_property, boost::listS>, boost::adj_list_edge_property_map<boost::undirected_tag, double,="" double&,="" long="" unsigned="" int,="" boost::property<boost::edge_weight_t,="" double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::edge_weight_t>, boost::iterator_property _map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc _impl<boost::undirected_tag,="" long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > >*, std::vector<std::vector<boost::detail::edge_d esc_impl<boost::undirected_tag,="" long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > >, std::allocator<std::vector<boost::detail::edge _desc_impl<boost::undirected_tag,="" long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > > > > >, boost::vec_adj_list_vertex_id_map<boost: :property<boost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > >, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int="">, std::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, long="" unsigned="" int=""> > >&>, boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, boost::vec_adj_list_ve rtex_id_map<boost::property<boost::vertex_index_t, int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, double, double&>, boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned="" int*,="" std::vector<long="" unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > >, boost::vec_adj_list_vertex_id_map<boost::property<b oost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, long unsigned int, long unsigned int&> >, boost::graph_visitor_t, boost::bgl_named_params <boost::iterator_property_map<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, boost::vec_adj_list_ve rtex_id_map<boost::property<boost::vertex_index_t, int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, double, double&>, boost::vertex_distance_t, boost::bgl_named_params<boost::vec_adj_list_ vertex_id_map<boost::property<boost::vertex_index_t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property=""> >, long unsigned int>, boost::vertex_index_t, boos t::bgl_named_params<boost::adj_list_edge_property_map<boost::undirecte d_tag,="" double,="" double&,="" long="" unsigned="" int,="" boost::property<boost::edge_weight_t,="" double,="" boost::property<boost::edge_centrality_t,="" double,="" boost::no_property=""> >, boost::edge_weight_t>, boost::edge_weight_t, boost::no_property> > > >]': boostIncl/boost/graph/dijkstra_shortest_paths.hpp:95: warning: 'bfs_vis$m_decreased' is used uninitialized in this function g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c cliques.cpp -o cliques.o cliques.cpp: In function 'void print_one_clique(oneCliqueType&)': cliques.cpp:110: warning: comparison between signed and unsigned integer expressions cliques.cpp: In function 'void print_all_cliques(allCliquesType&, char*)': cliques.cpp:118: warning: comparison between signed and unsigned integer expressions cliques.cpp: In function 'void extend_v2(Graph_ud&, std::vector<int, std::allocator<int=""> >&, std::vector<int, std::allocator<int=""> >&, int, int, int&, allCliquesType&)': cliques.cpp:139: warning: 's' may be used uninitialized in this function cliques.cpp:139: warning: 'pos' may be used uninitialized in this function cliques.cpp:138: warning: 'fixp' may be used uninitialized in this function cliques.cpp: At global scope: cliques.cpp:115: warning: 'void print_all_cliques(allCliquesType&, char*)' defined but not used g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c hcs.cpp -o hcs.o hcs.cpp: In function 'void output_graph_labels(const V_Label&, const char*)': hcs.cpp:27: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void build_subgraph(Cluster&, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)': hcs.cpp:62: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void remove_vertices(int, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)': hcs.cpp:117: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'dst cluster_distance(const Graph_ud&, V_Label&, int, V_Label&)': hcs.cpp:134: warning: comparison between signed and unsigned integer expressions hcs.cpp:138: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void adopt_singleton(const Graph_ud&, V_Label&, ClusterResult&)': hcs.cpp:206: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void remove_clusters(ClusterResult&, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)': hcs.cpp:248: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'void HCS_internal(const Graph_ud&, V_Label&, ClusterResult&)': hcs.cpp:288: warning: comparison between signed and unsigned integer expressions hcs.cpp: In function 'SEXPREC* HCS_loop(Graph_ud&, V_Label&)': hcs.cpp:363: warning: comparison between signed and unsigned integer expressions hcs.cpp:393: warning: comparison between signed and unsigned integer expressions hcs.cpp:397: warning: comparison between signed and unsigned integer expressions hcs.cpp:353: warning: unused variable 'found_new_cluster' boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list<boost::undirecteds, double="">, OutputIterator = std::back_insert_iterator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > >]': boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$m_value' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$m_value' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$D108232$m_value$D106029$m_target' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$D108232$m_value$D106029$m_source' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$m_value' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$m_value' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$D108232$m_value$D106029$m_target' is used uninitialized in this function boostIncl/boost/graph/detail/adjacency_list.hpp:262: warning: 'p$D108267$D108232$m_value$D106029$m_source' is used uninitialized in this function boostIncl/boost/graph/edge_connectivity.hpp:32: warning: 'p' may be used uninitialized in this function hcs.cpp: At global scope: hcs.cpp:24: warning: 'void output_graph_labels(const V_Label&, const char*)' defined but not used hcs.cpp:32: warning: 'void output_graph(const Graph_ud&, const char*)' defined but not used g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c incrConnComp.cpp -o incrConnComp.o incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXPREC*, SEXPREC*, SEXPREC*, E_IC_METHOD)': incrConnComp.cpp:67: warning: comparison between signed and unsigned integer expressions g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include -IboostIncl -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c interfaces.cpp -o interfaces.o interfaces.cpp: In function 'SEXPREC* BGL_articulation_points_U(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)': interfaces.cpp:311: warning: comparison between signed and unsigned integer expressions boostIncl/boost/graph/depth_first_search.hpp: In function 'void boost::depth_first_search(const VertexListGraph&, const boost::bgl_named_params<p, t,="" r="">&) [with VertexListGraph = std::vector<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> >, std::allocator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > > >, P = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<long unsigned="" int,="" std::allocator<long="" 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: instantiated from 'void boost::topological_sort(VertexListGraph&, OutputIterator, const boost::bgl_named_params<p, t,="" r="">&) [with VertexListGraph = std::vector<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> >, std::allocator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > > >, OutputIterator = std::back_insert_iterator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > >, P = boost::identity_property_map, T = boost::vertex_index_t, R = boost::no_property]' boostIncl/boost/graph/transitive_closure.hpp:120: instantiated 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<bgl_sequential_vertex_coloring::vertex_size_typ e*,="" boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_co="" lor_t,="" boost::default_color_type,="" boost::no_property="">, long unsigned int>, long unsigned int, long unsigned int&>, VertexIndexMap = boost:: vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type,="" boost::no_property="">, long unsigned int>]' boostIncl/boost/graph/transitive_closure.hpp:263: instantiated from 'void boost::transitive_closure(const Graph&, GraphTC&) [with Graph = Graph_dd, GraphTC = Graph_dd]' interfaces.cpp:371: instantiated from here boostIncl/boost/graph/depth_first_search.hpp:324: error: no matching function for call to 'vertices(const std::vector<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> >, std::allocator<std::vector<long unsigned="" int,="" std::allocator<long="" unsigned="" int=""> > > >&)' make: *** [interfaces.o] Error 1 chmod: cannot access `/usr/lib64/R/library/RBGL/libs/*': No such file or directory ERROR: compilation failed for package 'RBGL' ** Removing '/usr/lib64/R/library/RBGL'

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Hi, Johannes, Jeff and others, Getting back to this. It seems that there's some interplay among the header files which caused compilation errors (big time). I separated the troubled function (for transitive.closure) and I could go through w/o problems. The codes are in svn: RBGL1.9.2. If you have sometime, could you please try it and let me know if it works in your previous setting? Thanks a great deal! Li > hi all, > as far as i understood the boost library (or RBGL) bases mainly on templates, concerning this i found something at the gcc site > http://gcc.gnu.org/gcc-4.1/changes.html > > The (undocumented) extension which permitted templates with default arguments to be bound to template template parameters with fewer parameters > has been deprecated, and will be removed in the next major release of G++. For example: > > template <template <typename=""> class C> > void f(C<double>) {} > > template <typename t,="" typename="" u="int"> > struct S {}; > > template void f(S<double>); > > makes use of the deprecated extension. The reason this code is not valid ISO > C++ is that S is a template with two parameters; therefore, it cannot be bound to C which has only one parameter. > > if this is the reason that the package doesn't compile it won't work on systems with the gcc4.1 or later... > > jo > > On 5/11/06, Jeff Gentry <jgentry at="" jimmy.harvard.edu=""> wrote: >> >> > based on your suggestions i tested now some new settings, i used the >> gcc >> > 3.2.3 compiler (g++32 ) to compile the package (unfortunately there is >> no >> > 4.0 version available for FC5) and get, on my system with R 2.3 and RBGL_1.8.1 the same error as before. but interestingly the >> installation >> of >> > RBGL_1.6.0.tar.gz with the g++32 worked (but not with the g++ from gcc >> 4.1). >> > well, i guess i will have to try on... >> >> FWIW I have the same problem on my system (RHEL3, AMD64), and just looked >> and indeed it is gcc 3.2.3. >> >> > > > -- > Johannes Rainer, Msc > Tyrolean Cancer Research Institute > Innrain 66, 6020 Innsbruck, Austria > Tel.: +43 512 570485 15 > Email: johannes.rainer at tcri.at > johannes.rainer at tugraz.at > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >