Entering edit mode
Johannes Rainer
▴
300
@johannes-rainer-1676
Last seen 10.2 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'