Package: RBGL

Version: 1.35.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.35.0.tar.gz

StartedAt: 2013-03-25 04:05:35 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:08:50 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 195.2 seconds

RetCode: 0

Status:  OK

CheckDir: RBGL.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RBGL.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.35.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RBGL’ can be installed ... [127s/132s] OK
* checking installed package size ... NOTE
  installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
* checking package directory ... 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 ... [7s/7s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/RBGL.Rcheck/00check.log’
for details.

* installing *source* package ‘RBGL’ ...
untarring boost include tree...
** libs
g++ -I/home/biocbuild/bbs-2.12-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-2.12-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-2.12-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-2.12-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-2.12-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-2.12-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-2.12-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-2.12-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-2.12-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).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>::<anonymous>.boost::iterator_adaptor<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>, __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> > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__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).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>::<anonymous>.boost::iterator_adaptor<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>, __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> > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__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-2.12-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).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>::<anonymous>.boost::iterator_adaptor<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>, __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> > > > > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__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).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>::<anonymous>.boost::iterator_adaptor<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>, __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> > > > > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__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-2.12-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-2.12-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-2.12-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-2.12-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-2.12-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).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>::<anonymous>.boost::iterator_adaptor<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>, __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> > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__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).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>::<anonymous>.boost::iterator_adaptor<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>, __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> > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__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-2.12-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/lib -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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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)

name	user	system	elapsed
FileDep	1.168	0.028	1.218
astarSearch	0.024	0.008	0.029
bandwidth	0.06	0.00	0.06
bccluster	0.044	0.008	0.051
bellman.ford.sp	0.036	0.004	0.040
betweenness	0.04	0.00	0.04
bfs	0.088	0.008	0.096
biConnComp	0.028	0.004	0.034
chrobakPayneStraightLineDrawing	0.052	0.000	0.050
clusteringCoef	0.024	0.016	0.039
clusteringCoefAppr	0.028	0.012	0.042
coloring	0.016	0.012	0.027
connectedComp	0.052	0.004	0.060
dag.sp	0.044	0.000	0.046
dijkstra.sp	0.076	0.000	0.076
dominatorTree	0.032	0.004	0.034
edgeConn	0.024	0.008	0.029
edmondsMaxCardinalityMatching	0.104	0.012	0.119
edmondsOptimumBranching	0.060	0.020	0.078
extractPath	0.028	0.004	0.030
floyd.warshall.all.pairs.sp	0.016	0.012	0.030
gprofile	0.024	0.004	0.031
graphGenerator	0.012	0.004	0.016
highlyConnSG	0.028	0.004	0.033
incrConnComp	0.036	0.000	0.036
is.triangulated	0.032	0.016	0.048
isKuratowskiSubgraph	0.052	0.000	0.073
isStraightLineDrawing	0.040	0.016	0.053
isomorphism	0.032	0.012	0.045
johnson.all.pairs.sp	0.028	0.004	0.030
kCliques	0.020	0.004	0.028
kCores	0.080	0.008	0.090
lambdaSets	0.028	0.000	0.029
layout	0.020	0.000	0.018
makeBiconnectedPlanar	0.044	0.008	0.054
makeConnected	0.048	0.008	0.057
makeMaximalPlanar	0.036	0.008	0.043
maxClique	0.056	0.020	0.076
maxFlow	0.052	0.004	0.059
minCut	0.036	0.000	0.035
mstree.kruskal	0.108	0.008	0.117
mstree.prim	0.172	0.012	0.186
ordering	0.044	0.012	0.088
planarCanonicalOrdering	0.044	0.020	0.130
planarFaceTraversal	0.048	0.008	0.100
removeSelfLoops	0.040	0.004	0.091
separates	0.032	0.008	0.044
sp.between	0.068	0.008	0.075
strongComp	0.040	0.008	0.047
transClosure	0.032	0.000	0.030
transitivity	0.032	0.004	0.040
tsort	0.016	0.016	0.202
wavefront	0.016	0.016	0.036