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Package 477/609HostnameOS / ArchBUILDCHECKBUILD BIN
RBGL 1.34.0
Bioconductor Package Maintainer
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/RBGL
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: RBGL
Version: 1.34.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.34.0.tar.gz
StartedAt: 2013-03-25 04:09:00 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:12:14 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 194.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/RBGL.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘RBGL’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/RBGL.Rcheck/00check.log’
for details.

RBGL.Rcheck/00install.out:

* installing *source* package ‘RBGL’ ...
untarring boost include tree...
** libs
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c bbc.cpp -o bbc.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c cliques.cpp -o cliques.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c clusteringCoef.cpp -o clusteringCoef.o
clusteringCoef.cpp: In function ‘SEXPREC* graphGenerator(SEXP, SEXP, SEXP)’:
clusteringCoef.cpp:394:40: warning: ‘u’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c dominatorTree.cpp -o dominatorTree.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c hcs.cpp -o hcs.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp: In function ‘SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)’:
incrConnComp.cpp:74:6: warning: unused variable ‘child_index’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c interfaces.cpp -o interfaces.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c minST.cpp -o minST.o
In file included from minST.cpp:2:0:
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list<boost::directedS, double>, OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > >, Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, long unsigned int, long unsigned int&>, Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, long unsigned int, long unsigned int&>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)(& ei)+48).__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wuninitialized]
rbgl_trimmed_boost_1_49_0/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)(& ei)+48).__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ was declared here
rbgl_trimmed_boost_1_49_0/boost/graph/detail/edge.hpp:29:34: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ may be used uninitialized in this function [-Wuninitialized]
rbgl_trimmed_boost_1_49_0/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ was declared here
rbgl_trimmed_boost_1_49_0/boost/graph/kruskal_min_spanning_tree.hpp:48:5: warning: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c mincut.cpp -o mincut.o
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_max_flow_internal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, E_MF_METHOD)’:
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)(& ei)+48).__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >::_M_current’ may be used uninitialized in this function [-Wuninitialized]
mincut.cpp:99:19: note: ‘*((void*)(& ei)+48).__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >::_M_current’ was declared here
mincut.cpp:103:54: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c ordering.cpp -o ordering.o
ordering.cpp: In function ‘SEXPREC* BGL_king_ordering(SEXP, SEXP, SEXP, SEXP)’:
ordering.cpp:180:48: warning: variable ‘id’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c planar.cpp -o planar.o
planar.cpp: In function ‘SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)’:
planar.cpp:161:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
planar.cpp:165:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
planar.cpp: In function ‘SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)’:
planar.cpp:256:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
planar.cpp:225:34: warning: variable ‘oi_end’ set but not used [-Wunused-but-set-variable]
planar.cpp: In function ‘SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)’:
planar.cpp:369:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
planar.cpp: In function ‘SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)’:
planar.cpp:429:36: warning: variable ‘ki_end’ set but not used [-Wunused-but-set-variable]
planar.cpp:461:6: warning: unused variable ‘i’ [-Wunused-variable]
In file included from planar.cpp:5:0:
rbgl_trimmed_boost_1_49_0/boost/graph/planar_canonical_ordering.hpp: In function ‘void boost::planar_canonical_ordering(const Graph&, PlanarEmbedding, OutputIterator, VertexIndexMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >, PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<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> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int> >, OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/planar_canonical_ordering.hpp:149:17: warning: ‘second_vertex’ may be used uninitialized in this function [-Wuninitialized]
In file included from planar.cpp:11:0:
rbgl_trimmed_boost_1_49_0/boost/graph/max_cardinality_matching.hpp: In member function ‘bool boost::edmonds_augmenting_path_finder<Graph, MateMap, VertexIndexMap>::augment_matching() [with Graph = R_adjacency_list<boost::undirectedS, int>, MateMap = long unsigned int*, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/max_cardinality_matching.hpp:334:7: warning: ‘w’ may be used uninitialized in this function [-Wuninitialized]
rbgl_trimmed_boost_1_49_0/boost/graph/max_cardinality_matching.hpp:333:7: warning: ‘v’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c shortestPath.cpp -o shortestPath.o
In file included from shortestPath.cpp:4:0:
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp: In function ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>, DistanceMatrix = Basic2DMatrix<double>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, BinaryPredicate = std::less<double>, BinaryFunction = boost::closed_plus<double>, Infinity = double, DistanceZero = double]’:
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:171:67:   instantiated from ‘bool boost::detail::johnson_dispatch(VertexAndEdgeListGraph&, DistanceMatrix&, const boost::bgl_named_params<P, T, R>&, Weight, VertexID) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>, DistanceMatrix = Basic2DMatrix<double>, P = int, T = int, R = boost::no_property, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:198:63:   instantiated from ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>, DistanceMatrix = Basic2DMatrix<double>]’
shortestPath.cpp:56:46:   instantiated from here
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:124:49: warning: variable ‘u1’ set but not used [-Wunused-but-set-variable]
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:124:53: warning: variable ‘v1’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c sna.cpp -o sna.o
sna.cpp: In function ‘SEXPREC* lambdaSets(SEXP, SEXP, SEXP, SEXP)’:
sna.cpp:161:9: warning: variable ‘res_cap’ set but not used [-Wunused-but-set-variable]
In file included from sna.cpp:3:0:
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp: In function ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>, DistanceMatrix = Basic2DMatrix<double>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, BinaryPredicate = std::less<double>, BinaryFunction = boost::closed_plus<double>, Infinity = double, DistanceZero = double]’:
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:171:67:   instantiated from ‘bool boost::detail::johnson_dispatch(VertexAndEdgeListGraph&, DistanceMatrix&, const boost::bgl_named_params<P, T, R>&, Weight, VertexID) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>, DistanceMatrix = Basic2DMatrix<double>, P = int, T = int, R = boost::no_property, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:198:63:   instantiated from ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>, DistanceMatrix = Basic2DMatrix<double>]’
sna.cpp:105:46:   instantiated from here
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:124:49: warning: variable ‘u1’ set but not used [-Wunused-but-set-variable]
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:124:53: warning: variable ‘v1’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c transitive_closure.cpp -o transitive_closure.o
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_transitive_closure_D(SEXP, SEXP, SEXP)’:
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)(& ei)+48).__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wuninitialized]
transitive_closure.cpp:43:33: note: ‘*((void*)(& ei)+48).__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ was declared here
transitive_closure.cpp:46:50: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c wavefront.cpp -o wavefront.o
g++ -shared -L/usr/local/lib64 -o RBGL.so bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o shortestPath.o sna.o transitive_closure.o wavefront.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/RBGL.Rcheck/RBGL/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RBGL.Rnw’ 
** testing if installed package can be loaded

* DONE (RBGL)

RBGL.Rcheck/RBGL-Ex.timings:

nameusersystemelapsed
FileDep0.8040.0281.211
astarSearch0.0120.0000.029
bandwidth0.020.000.02
bccluster0.0160.0000.016
bellman.ford.sp0.0120.0040.016
betweenness0.0120.0000.012
bfs0.0240.0040.035
biConnComp0.0160.0000.014
chrobakPayneStraightLineDrawing0.0120.0000.013
clusteringCoef0.0160.0000.043
clusteringCoefAppr0.0120.0000.011
coloring0.0080.0000.019
connectedComp0.0280.0000.093
dag.sp0.0160.0000.032
dijkstra.sp0.0320.0000.044
dominatorTree0.0080.0000.010
edgeConn0.0120.0000.012
edmondsMaxCardinalityMatching0.0120.0040.020
edmondsOptimumBranching0.0080.0000.010
extractPath0.0080.0000.007
floyd.warshall.all.pairs.sp0.0120.0000.011
gprofile0.0080.0000.009
graphGenerator0.0040.0000.001
highlyConnSG0.0080.0040.014
incrConnComp0.0120.0000.013
is.triangulated0.020.000.05
isKuratowskiSubgraph0.0200.0000.019
isStraightLineDrawing0.0160.0000.015
isomorphism0.0240.0000.025
johnson.all.pairs.sp0.0120.0040.013
kCliques0.0200.0000.019
kCores0.0680.0040.075
lambdaSets0.0080.0080.019
layout000
makeBiconnectedPlanar0.0240.0000.023
makeConnected0.0120.0000.014
makeMaximalPlanar0.0160.0000.019
maxClique0.0200.0040.060
maxFlow0.0200.0000.048
minCut0.0080.0000.010
mstree.kruskal0.0360.0000.093
mstree.prim0.0240.0000.057
ordering0.0120.0000.016
planarCanonicalOrdering0.0120.0000.036
planarFaceTraversal0.0120.0000.029
removeSelfLoops0.0160.0000.041
separates0.0240.0000.036
sp.between0.0440.0040.087
strongComp0.020.000.02
transClosure0.0200.0000.037
transitivity0.0080.0000.026
tsort0.0000.0040.006
wavefront0.0120.0000.030