[BioC] RBGL 1.8.1 installation error on linux

Johannes Rainer johannes.rainer at tcri.at
Thu May 11 11:25:45 CEST 2006


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<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_vertex_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_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>, Params = boost::bgl_named_params<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_desc_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_vertex_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<boost::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_vertex_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, boost::bgl_named_params<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::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_Type*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_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_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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