RBGL 1.8.1 installation error on linux
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@johannes-rainer-1676
Last seen 7.1 years ago
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'
Cancer graph RBGL Cancer graph RBGL • 1.2k views
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@johannes-rainer-1676
Last seen 7.1 years ago
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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Pretty much all the msgs are about templates, so I would look more into what your g++/STL and the likes on your machine. Li > 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 > _______________________________________________ > 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
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Hi, Johannes Rainer wrote: > ok now i tested some other things. on a system (FC4) with the gcc 4.0 there > is no problem installing the package. could it be that it does not work with > gcc4.1? (although it compiles the source files neatly, but after the > compilation it gets that error). Yes, it is entirely possible that such versions of gcc will fail on something as heavily templated as BGL. gcc tends to be somewhat unstable for versions near the bleeding edge. You do not need a copy of BGL, it is included in the sources for the package and in fact, having a copy around could cause some problems as I think we (Li) have to patch from time to time (right now I think a header file) and if you compile against the wrong one bad things are going to happen. I has nothing to do with 64bit, we build on that, but Suse not Redhat. > i edited also the Makeconf file located in /usr/lib64/R/etc and set the the > CXXFLAGS to CXXFLAGS = -O2 -g -m64. nothing worked (i only got less warnings > during the compilation). > actually i run out of ideas what i could try next... Use a version of gcc that is known to work? Your tests and ours have indicated that gcc 4.0.x does work. I am afraid this looks like a redhat/gcc problem and you might want to take it up with them. best wishes Robert ps Li, I am not seeing your responses could you please make sure that they are too the list, this is archived and many find it useful to be able to follow the whole thread > > jo > > > On 5/11/06, Li.Long at isb-sib.ch <li.long at="" isb-sib.ch=""> wrote: >> >> That's right version. boost lib is packaged in RBGL. That's not what I >> would worry about. >> >> Li >> >>> which version of the boost library do i need? i have boost 1.33.1 >>> >>> jo >>> >>> On 5/11/06, Li.Long at isb-sib.ch <li.long at="" isb-sib.ch=""> wrote: >>>> >>>> Pretty much all the msgs are about templates, so I would look more into >>>> what your g++/STL and the likes on your machine. >>>> >>>> Li >>>> >>>>> 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 >>>>> _______________________________________________ >>>>> 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 >>> >> > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Hi, Johannes Rainer wrote: > hi, > > thanks robert for your help. > 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 Hmm, I don't think that is the right set of numbers for a gcc compiler, 4.0.3 and 3.4.5 are the up to date versions are reported at: http://gcc.gnu.org/. I don't know why there would not be a version of all for FC5, certainly there were discussions of it and some of the early work on FC5 was based on the 4.0 arm (4.1 is very new, released 2006-02-28). You should be able to build these from source if you wanted to. I remain convinced that these are likely compiler bugs and hence someone at Redhat or gcc might care, we are not really able to do much about them. Sorry we don't have such a beast here for any testing so I cannot say much more that would be helpful. best wishes Robert > 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... > > thanks for your help > jo > > On 5/11/06, *rgentlem* <rgentlem at="" fhcrc.org="" <mailto:rgentlem="" at="" fhcrc.org="">> > wrote: > > Hi, > > Johannes Rainer wrote: > > ok now i tested some other things. on a system (FC4) with the gcc > 4.0 there > > is no problem installing the package. could it be that it does > not work with > > gcc4.1? (although it compiles the source files neatly, but after the > > compilation it gets that error). > > Yes, it is entirely possible that such versions of gcc will fail on > something as heavily templated as BGL. gcc tends to be somewhat unstable > for versions near the bleeding edge. > > You do not need a copy of BGL, it is included in the sources for the > package and in fact, having a copy around could cause some problems as I > think we (Li) have to patch from time to time (right now I think a > header file) and if you compile against the wrong one bad things are > going to happen. > > I has nothing to do with 64bit, we build on that, but Suse not Redhat. > > > i edited also the Makeconf file located in /usr/lib64/R/etc and > set the the > > CXXFLAGS to CXXFLAGS = -O2 -g -m64. nothing worked (i only got > less warnings > > during the compilation). > > actually i run out of ideas what i could try next... > > Use a version of gcc that is known to work? Your tests and ours have > indicated that gcc 4.0.x does work. I am afraid this looks like a > redhat/gcc problem and you might want to take it up with them. > > best wishes > Robert > > ps Li, I am not seeing your responses could you please make sure that > they are too the list, this is archived and many find it useful to be > able to follow the whole thread > > > > > jo > > > > > > On 5/11/06, Li.Long at isb-sib.ch <mailto:li.long at="" isb-="" sib.ch=""> > <li.long at="" isb-sib.ch="" <mailto:li.long="" at="" isb-sib.ch="">> wrote: > >> > >> That's right version. boost lib is packaged in RBGL. That's > not what I > >> would worry about. > >> > >> Li > >> > >>> which version of the boost library do i need? i have boost 1.33.1 > >>> > >>> jo > >>> > >>> On 5/11/06, Li.Long at isb-sib.ch <mailto:li.long at="" isb-="" sib.ch=""> > <li.long at="" isb-sib.ch="" <mailto:li.long="" at="" isb-sib.ch="">> wrote: > >>>> > >>>> Pretty much all the msgs are about templates, so I would look > more into > >>>> what your g++/STL and the likes on your machine. > >>>> > >>>> Li > >>>> > >>>>> 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 <mailto:li.long at="" isb-="" sib.ch=""> > <li.long at="" isb-sib.ch="" <mailto: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 <mailto:johannes.rainer at="" tcri.at=""> > >>>>>>> johannes.rainer at tugraz.at > <mailto:johannes.rainer at="" tugraz.at=""> > >>>>>>> _______________________________________________ > >>>>>>> Bioconductor mailing list > >>>>>>> Bioconductor at stat.math.ethz.ch > <mailto: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 <mailto:johannes.rainer at="" tcri.at=""> > >>>>> johannes.rainer at tugraz.at > <mailto:johannes.rainer at="" tugraz.at=""> > >>>>> _______________________________________________ > >>>>> Bioconductor mailing list > >>>>> Bioconductor at stat.math.ethz.ch > <mailto: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 > <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 <mailto:johannes.rainer at="" tcri.at=""> > >>> johannes.rainer at tugraz.at > <mailto:johannes.rainer at="" tugraz.at=""> > >>> > >> > > > > > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org <mailto:rgentlem at="" fhcrc.org=""> > > > > > -- > Johannes Rainer, Msc > Tyrolean Cancer Research Institute > Innrain 66, 6020 Innsbruck, Austria > Tel.: +43 512 570485 15 > Email: johannes.rainer at tcri.at <mailto:johannes.rainer at="" tcri.at=""> > johannes.rainer at tugraz.at <mailto:johannes.rainer at="" tugraz.at=""> -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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On Thu, 2006-05-11 at 09:46 -0700, rgentlem wrote: > Hi, > > Johannes Rainer wrote: > > hi, > > > > thanks robert for your help. > > 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 > > Hmm, > I don't think that is the right set of numbers for a gcc compiler, > 4.0.3 and 3.4.5 are the up to date versions are reported at: > http://gcc.gnu.org/. > > I don't know why there would not be a version of all for FC5, > certainly there were discussions of it and some of the early work on FC5 > was based on the 4.0 arm (4.1 is very new, released 2006-02-28). You > should be able to build these from source if you wanted to. > > I remain convinced that these are likely compiler bugs and hence > someone at Redhat or gcc might care, we are not really able to do much > about them. Sorry we don't have such a beast here for any testing so I > cannot say much more that would be helpful. > best wishes > Robert I have the same setup as Johannes (FC5 on amd64), and I'm getting exactly the same error. The full output is show below, there are around 5 errors in there. > getBioC('RBGL') Running getBioC version 0.1.6 with R version 2.3.0 Running biocinstall version 1.8.2 with R version 2.3.0 Your version of R requires version 1.8 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.8/bioc/src/contrib/RBGL_1.8.1.tar. gz' Content type 'application/x-gzip' length 1460061 bytes opened URL ================================================== downloaded 1425Kb * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include - I/usr/local/include -IboostIncl -fpic -g -O2 -c bbc.cpp -o bbc.o g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include - I/usr/local/include -IboostIncl -fpic -g -O2 -c cliques.cpp -o cliques.o g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include - I/usr/local/include -IboostIncl -fpic -g -O2 -c hcs.cpp -o hcs.o g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include - I/usr/local/include -IboostIncl -fpic -g -O2 -c incrConnComp.cpp -o incrConnComp.o g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include - I/usr/local/include -IboostIncl -fpic -g -O2 -c interfaces.cpp -o interfaces.o 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_si ze_type*,="" boost::vec_adj_list_vertex_id_map<boost::property<boost::ver="" tex_color_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_colo r_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/local/lib64/R/library/RBGL/libs/*': No such file or directory ERROR: compilation failed for package 'RBGL' ** Removing '/usr/local/lib64/R/library/RBGL > sessionInfo() Version 2.3.0 (2006-04-24) x86_64-unknown-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" [francois at flims tmp]$ gcc --version gcc (GCC) 4.1.0 20060304 (Red Hat 4.1.0-3)
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> 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.
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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 >
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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 >
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Hi Li, great! I just managed to install RBGL 1.9.2 from svn revision 18245, on a computer with gcc 4.1.0, without compiler errors, and to attach the library. > sessionInfo() Version 2.3.1 RC (2006-05-29 r38219) x86_64-unknown-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: RBGL graph Ruuid "1.9.2" "1.10.4" "1.10.0" huber at boltzmann:~/madman/Rpacks> uname -a Linux boltzmann 2.6.16.13-4-smp #1 SMP Wed May 3 04:53:23 UTC 2006 x86_64 x86_64 x86_64 GNU/Linux huber at boltzmann:~/madman/Rpacks> gcc --version gcc (GCC) 4.1.0 (SUSE Linux) PS there was only one warning, from sna.cpp: g++ -I/home/huber/R-rc/include -I/home/huber/R-rc/include -I/usr/local/include -IboostIncl -fpic -O3 -c sna.cpp -o sna.o sna.cpp: In function ?SEXPREC* lambdaSets(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC* )?: sna.cpp:204: warning: converting to ?int? from ?double? ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Li.Long at isb-sib.ch wrote: > 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 > >
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> Hi Li, > > great! I just managed to install RBGL 1.9.2 from svn revision 18245, on > a computer with gcc 4.1.0, without compiler errors, and to attach the > library. Thanks, good to know it works for others as well :) > PS there was only one warning, from sna.cpp: > > g++ -I/home/huber/R-rc/include -I/home/huber/R-rc/include > -I/usr/local/include -IboostIncl -fpic -O3 -c sna.cpp -o sna.o > sna.cpp: In function ???SEXPREC* lambdaSets(SEXPREC*, SEXPREC*, SEXPREC*, > SEXPREC* )???: > sna.cpp:204: warning: converting to ???int??? from ???double??? I know this. Since it's of no harm, I just haven't done much about it yet :( Thanks Li
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