ecs2a[ckc]56: bsub -Is -mturing -qhugemem -Ppathogen-microarrays -R"select[mem>16000]rusage[mem=16000]" /usr/local/R-2.3.0/bin/R CMD INSTALL -l /nfs/pombeaffy/mq2/bioconductor/ /nfs/pombeaffy/mq2/bioconductor/RBGL_1.8.1.tar.gz 
Job <374696> is submitted to queue <hugemem>.
<<Waiting for dispatch ...>>
<<Starting on turing>>
* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
/tmp/ccc73h5A.s: Assembler messages:
/tmp/ccc73h5A.s:9306: Warning: Additional NOP may be necessary to workaround Itanium processor A/B step errata
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c cliques.cpp -o cliques.o
/tmp/cc4i4Gbh.s: Assembler messages:
/tmp/cc4i4Gbh.s:8537: Warning: Use of 'mov' may violate WAW dependency 'GR%, % in 1 - 127' (impliedf), specific resource number is 15
/tmp/cc4i4Gbh.s:8537: Warning: Only the first path encountering the conflict is reported
/tmp/cc4i4Gbh.s:8536: Warning: This is the location of the conflicting usage
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c hcs.cpp -o hcs.o
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c incrConnComp.cpp -o incrConnComp.o
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c interfaces.cpp -o interfaces.o
boostIncl/boost/graph/biconnected_components.hpp: In function 
   `std::pair<size_t, OutputIterator> boost::biconnected_components(const 
   Graph&, ComponentMap, OutputIterator, DiscoverTimeMap, LowPointMap, 
   PredecessorMap, VertexIndexMap) [with Graph = 
   R_adjacency_list<boost::undirectedS, double>, ComponentMap = 
   boost::dummy_property_map, OutputIterator = 
   std::back_insert_iterator<std::vector<size_t, std::allocator<size_t> > >, 
   DiscoverTimeMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, LowPointMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, PredecessorMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, 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>, size_t>]':
ecs2a[ckc]56: bsub -Is -mturing -qhugemem -Ppathogen-microarrays -R"select[mem>16000]rusage[mem=16000]" /usr/local/R-2.3.0/bin/R CMD INSTALL -l /nfs/pombeaffy/mq2/bioconductor/ /nfs/pombeaffy/mq2/bioconductor/RBGL_1.8.1.tar.gz 
Job <374696> is submitted to queue <hugemem>.
<<Waiting for dispatch ...>>
<<Starting on turing>>
* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
/tmp/ccc73h5A.s: Assembler messages:
/tmp/ccc73h5A.s:9306: Warning: Additional NOP may be necessary to workaround Itanium processor A/B step errata
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c cliques.cpp -o cliques.o
/tmp/cc4i4Gbh.s: Assembler messages:
/tmp/cc4i4Gbh.s:8537: Warning: Use of 'mov' may violate WAW dependency 'GR%, % in 1 - 127' (impliedf), specific resource number is 15
/tmp/cc4i4Gbh.s:8537: Warning: Only the first path encountering the conflict is reported
/tmp/cc4i4Gbh.s:8536: Warning: This is the location of the conflicting usage
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c hcs.cpp -o hcs.o
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c incrConnComp.cpp -o incrConnComp.o
g++ -I/usr/local/R-2.3.0/lib/R/include -I/usr/local/R-2.3.0/lib/R/include  -I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c interfaces.cpp -o interfaces.o
boostIncl/boost/graph/biconnected_components.hpp: In function 
   `std::pair<size_t, OutputIterator> boost::biconnected_components(const 
   Graph&, ComponentMap, OutputIterator, DiscoverTimeMap, LowPointMap, 
   PredecessorMap, VertexIndexMap) [with Graph = 
   R_adjacency_list<boost::undirectedS, double>, ComponentMap = 
   boost::dummy_property_map, OutputIterator = 
   std::back_insert_iterator<std::vector<size_t, std::allocator<size_t> > >, 
   DiscoverTimeMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, LowPointMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, PredecessorMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, 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>, size_t>]':
boostIncl/boost/graph/biconnected_components.hpp:170:   instantiated from `std::pair<size_t, OutputIterator> boost::biconnected_components(const Graph&, ComponentMap, OutputIterator, DiscoverTimeMap, LowPointMap, VertexIndexMap) [with Graph = R_adjacency_list<boost::undirectedS, double>, ComponentMap = boost::dummy_property_map, OutputIterator = std::back_insert_iterator<std::vector<size_t, std::allocator<size_t> > >, DiscoverTimeMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, std::vector<size_t, std::allocator<size_t> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, size_t>, long unsigned int, long unsigned int&>, LowPointMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, std::vector<size_t, std::allocator<size_t> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, size_t>, 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>, size_t>]'
boostIncl/boost/graph/biconnected_components.hpp:191:   instantiated from `std::pair<size_t, OutputIterator> boost::biconnected_components(const Graph&, ComponentMap, OutputIterator, VertexIndexMap) [with Graph = R_adjacency_list<boost::undirectedS, double>, ComponentMap = boost::dummy_property_map, OutputIterator = std::back_insert_iterator<std::vector<size_t, std::allocator<size_t> > >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, size_t>]'
boostIncl/boost/graph/biconnected_components.hpp:245:   instantiated from `OutputIterator boost::articulation_points(const Graph&, OutputIterator) [with Graph = Graph_ud, OutputIterator = std::back_insert_iterator<std::vector<size_t, std::allocator<size_t> > >]'
interfaces.cpp:302:   instantiated from here
boostIncl/boost/graph/biconnected_components.hpp:154: no matching function for 
   call to `
   boost::bgl_named_params<boost::detail::biconnected_components_visitor<boost::dummy_property_map,
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >,
   _property_map, OutputIterator = std::back_insert_iterator<std::vector<size_t, std::allocator<size_t> > >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, size_t>]'
boostIncl/boost/graph/biconnected_components.hpp:245:   instantiated from `OutputIterator boost::articulation_points(const Graph&, OutputIterator) [with Graph = Graph_ud, OutputIterator = std::back_insert_iterator<std::vector<size_t, std::allocator<size_t> > >]'
interfaces.cpp:302:   instantiated from here
boostIncl/boost/graph/biconnected_components.hpp:154: no matching function for 
   call to `
   boost::bgl_named_params<boost::detail::biconnected_components_visitor<boost::dummy_property_map,
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, std::back_insert_iterator<std::vector<size_t, 
   std::allocator<size_t> > >, 
   std::stack<boost::detail::edge_desc_impl<boost::undirected_tag, size_t>, 
   std::deque<boost::detail::edge_desc_impl<boost::undirected_tag, size_t>, 
   std::allocator<BGL_edge_connectivity_U(SEXPREC*, SEXPREC*, SEXPREC*, 
   SEXPREC*)::Edge> > > >, boost::graph_visitor_t, boost::no_property>::
   vertex_index_map(
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>&)'
boostIncl/boost/graph/biconnected_components.hpp: In function 
   `std::pair<size_t, OutputIterator> boost::biconnected_components(const 
   Graph&, ComponentMap, OutputIterator, DiscoverTimeMap, LowPointMap, 
   PredecessorMap, VertexIndexMap) [with Graph = 
   R_adjacency_list<boost::undirectedS, double>, ComponentMap = 
   boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, 
   size_t, boost::property<boost::edge_weight_t, double, boost::no_property>, 
   boost::edge_weight_t>, OutputIterator = 
   boost::graph_detail::dummy_output_iterator, DiscoverTimeMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, LowPointMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, PredecessorMap = 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, 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>, size_t>]':
boostIncl/boost/graph/biconnected_components.hpp:170:   instantiated from `std::pair<size_t, OutputIterator> boost::biconnected_components(const Graph&, ComponentMap, OutputIterator, DiscoverTimeMap, LowPointMap, VertexIndexMap) [with Graph = R_adjacency_list<boost::undirectedS, double>, ComponentMap = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, size_t, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, OutputIterator = boost::graph_detail::dummy_output_iterator, DiscoverTimeMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, std::vector<size_t, std::allocator<size_t> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, size_t>, long unsigned int, long unsigned int&>, LowPointMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, std::vector<size_t, std::allocator<size_t> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, size_t>, 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>, size_t>]'
boostIncl/boost/graph/biconnected_components.hpp:191:   instantiated from `std::pair<size_t, OutputIterator> boost::biconnected_components(const Graph&, ComponentMap, OutputIterator, VertexIndexMap) [with Graph = R_adjacency_list<boost::undirectedS, double>, ComponentMap = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, size_t, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, OutputIterator = boost::graph_detail::dummy_output_iterator, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, size_t>]'
boostIncl/boost/graph/biconnected_components.hpp:202:   instantiated from `std::pair<size_t, OutputIterator> boost::biconnected_components(const Graph&, ComponentMap, OutputIterator) [with Graph = R_adjacency_list<boost::undirectedS, double>, ComponentMap = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, size_t, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, OutputIterator = boost::graph_detail::dummy_output_iterator]'
boostIncl/boost/graph/biconnected_components.hpp:228:   instantiated from `size_t boost::biconnected_components(const Graph&, ComponentMap) [with Graph = Graph_ud, ComponentMap = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, size_t, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>]'
interfaces.cpp:265:   instantiated from here
boostIncl/boost/graph/biconnected_components.hpp:154: no matching function for 
   call to `
   boost::bgl_named_params<boost::detail::biconnected_components_visitor<boost::adj_list_edge_property_map<boost::undirected_tag,
   double, double&, size_t, boost::property<boost::edge_weight_t, double, 
   boost::no_property>, boost::edge_weight_t>, 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, 
   boost::iterator_property_map<__gnu_cxx::__normal_iterator<size_t*, 
   std::vector<size_t, std::allocator<size_t> > >, 
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>, long unsigned int, 
   long unsigned int&>, boost::graph_detail::dummy_output_iterator, 
   std::stack<boost::detail::edge_desc_impl<boost::undirected_tag, size_t>, 
   std::deque<boost::detail::edge_desc_impl<boost::undirected_tag, size_t>, 
   std::allocator<BGL_edge_connectivity_U(SEXPREC*, SEXPREC*, SEXPREC*, 
   SEXPREC*)::Edge> > > >, boost::graph_visitor_t, boost::no_property>::
   vertex_index_map(
   boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, 
   boost::default_color_type, boost::no_property>, size_t>&)'
make: *** [interfaces.o] Error 1
chmod: failed to get attributes of `/.automount/pcs3/root/nfs/pombeaffy/mq2/bioconductor/RBGL/libs/*': No such file or directory
ERROR: compilation failed for package 'RBGL'
** Removing '/.automount/pcs3/root/nfs/pombeaffy/mq2/bioconductor/RBGL'
