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BioC 3.2: CHECK report for RBGL on moscato1

This page was generated on 2016-04-23 10:15:20 -0700 (Sat, 23 Apr 2016).

Package 842/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.46.0
Bioconductor Package Maintainer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RBGL
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.46.0
Command: rm -rf RBGL.buildbin-libdir RBGL.Rcheck && mkdir RBGL.buildbin-libdir RBGL.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RBGL.buildbin-libdir RBGL_1.46.0.tar.gz >RBGL.Rcheck\00install.out 2>&1 && cp RBGL.Rcheck\00install.out RBGL-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RBGL.buildbin-libdir --install="check:RBGL-install.out" --force-multiarch --no-vignettes --timings RBGL_1.46.0.tar.gz
StartedAt: 2016-04-23 06:28:38 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:39:37 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 659.0 seconds
RetCode: 0
Status:  OK  
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RBGL.buildbin-libdir RBGL.Rcheck && mkdir RBGL.buildbin-libdir RBGL.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RBGL.buildbin-libdir RBGL_1.46.0.tar.gz >RBGL.Rcheck\00install.out 2>&1 && cp RBGL.Rcheck\00install.out RBGL-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RBGL.buildbin-libdir --install="check:RBGL-install.out" --force-multiarch --no-vignettes --timings RBGL_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/RBGL.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.46.0'
* 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 whether package 'RBGL' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'RBGL/R/zzz.R':
  .onLoad calls:
    require("methods")

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/RBGL.buildbin-libdir/RBGL/libs/i386/RBGL.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/RBGL.buildbin-libdir/RBGL/libs/x64/RBGL.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [3s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [1s]
 [2s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [2s]
 [2s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/RBGL.Rcheck/00check.log'
for details.

RBGL.Rcheck/00install.out:


install for i386

* installing *source* package 'RBGL' ...
found  rbgl_trimmed_boost_1_49_0  header sources and tar archive;\n using what is there.
** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c bbc.cpp -o bbc.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c cliques.cpp -o cliques.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c dominatorTree.cpp -o dominatorTree.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c hcs.cpp -o hcs.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c interfaces.cpp -o interfaces.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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, unsigned int> > >, Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, unsigned int>, unsigned int, unsigned int&>, Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, unsigned int>, unsigned int, unsigned int&>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, 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)+24).__gnu_cxx::__normal_iterator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<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)+24).__gnu_cxx::__normal_iterator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<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)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, unsigned int>, 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)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, unsigned int>, int>::m_src' was declared here
rbgl_trimmed_boost_1_49_0/boost/graph/kruskal_min_spanning_tree.hpp:48:5: warning: '*((void*)(& ei)+16).__gnu_cxx::__normal_iterator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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)+24).__gnu_cxx::__normal_iterator<boost::detail::sep_<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, unsigned int> > > > >*, std::vector<boost::detail::sep_<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, unsigned int> > > > >, std::allocator<boost::detail::sep_<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, unsigned int> > > > > > > >::_M_current' may be used uninitialized in this function [-Wuninitialized]
mincut.cpp:99:19: note: '*((void*)(& ei)+24).__gnu_cxx::__normal_iterator<boost::detail::sep_<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, unsigned int> > > > >*, std::vector<boost::detail::sep_<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, unsigned int> > > > >, std::allocator<boost::detail::sep_<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, unsigned int> > > > > > > >::_M_current' was declared here
mincut.cpp:103:54: warning: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<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, unsigned int> > > > >*, std::vector<boost::detail::sep_<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, unsigned int> > > > >, std::allocator<boost::detail::sep_<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, unsigned int> > > > > > > >, unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, unsigned int>, int>::m_src' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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, unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, unsigned int> >, OutputIterator = std::back_insert_iterator<std::vector<unsigned int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, 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 = unsigned int*, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, 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++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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>, unsigned int>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, 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&, 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>, 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++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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>, unsigned int>, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, 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&, 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>, 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++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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)+24).__gnu_cxx::__normal_iterator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<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)+24).__gnu_cxx::__normal_iterator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<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)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, unsigned int>, int>::m_src' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c wavefront.cpp -o wavefront.o
g++ -m32 -shared -s -static-libgcc -o RBGL.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/RBGL.buildbin-libdir/RBGL/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RBGL' ...
found  rbgl_trimmed_boost_1_49_0  header sources and tar archive;\n using what is there.
** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c bbc.cpp -o bbc.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c cliques.cpp -o cliques.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c dominatorTree.cpp -o dominatorTree.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c hcs.cpp -o hcs.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c interfaces.cpp -o interfaces.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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 long unsigned int> > >, Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long long unsigned int>, long long unsigned int, long long unsigned int&>, Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long long unsigned int>, long long unsigned int, long long unsigned int&>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long 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 long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long 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 long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long 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 long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, long 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 long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, long 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 long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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 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 long unsigned int> > > > >*, std::vector<boost::detail::sep_<long 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 long unsigned int> > > > >, std::allocator<boost::detail::sep_<long 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 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 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 long unsigned int> > > > >*, std::vector<boost::detail::sep_<long 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 long unsigned int> > > > >, std::allocator<boost::detail::sep_<long 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 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 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 long unsigned int> > > > >*, std::vector<boost::detail::sep_<long 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 long unsigned int> > > > >, std::allocator<boost::detail::sep_<long 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 long unsigned int> > > > > > > >, long long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, long long int>::m_src' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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 long unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long long unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long long unsigned int> >, OutputIterator = std::back_insert_iterator<std::vector<long long unsigned int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long 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 long unsigned int*, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long 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++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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 long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long 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 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 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++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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 long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long 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 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 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++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -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 long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long 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 long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long 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 long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long long unsigned int>, long long int>::m_src' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -Irbgl_trimmed_boost_1_49_0   -O2 -Wall  -mtune=core2 -c wavefront.cpp -o wavefront.o
g++ -m64 -shared -s -static-libgcc -o RBGL.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/RBGL.buildbin-libdir/RBGL/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RBGL' as RBGL_1.46.0.zip
* DONE (RBGL)

RBGL.Rcheck/examples_i386/RBGL-Ex.timings:

nameusersystemelapsed
FileDep0.600.000.62
astarSearch0.020.000.02
bandwidth0.020.000.02
bccluster0.010.000.01
bellman.ford.sp000
betweenness000
bfs0.020.000.01
biConnComp0.010.000.02
chrobakPayneStraightLineDrawing0.020.000.02
clusteringCoef0.020.000.01
clusteringCoefAppr000
coloring0.080.000.07
connectedComp0.010.001.28
dag.sp0.020.000.02
dijkstra.sp0.020.000.01
dominatorTree0.010.000.02
edgeConn000
edmondsMaxCardinalityMatching0.020.000.02
edmondsOptimumBranching0.010.000.01
extractPath0.000.010.02
floyd.warshall.all.pairs.sp0.020.000.01
gprofile0.010.000.02
graphGenerator000
highlyConnSG0.020.000.01
incrConnComp000
is.triangulated0.010.000.02
isKuratowskiSubgraph0.020.000.02
isStraightLineDrawing0.010.000.02
isomorphism0.020.000.01
johnson.all.pairs.sp000
kCliques000
kCores0.050.000.04
lambdaSets000
layout000
makeBiconnectedPlanar0.020.000.01
makeConnected000
makeMaximalPlanar0.010.000.02
maxClique0.030.000.03
maxFlow0.020.000.01
minCut0.010.000.02
mstree.kruskal0.030.000.03
mstree.prim000
ordering0.020.000.01
planarCanonicalOrdering000
planarFaceTraversal0.020.000.01
removeSelfLoops0.010.000.02
separates0.020.000.01
sp.between0.010.000.02
strongComp0.020.000.02
transClosure0.010.000.01
transitivity000
tsort0.020.000.02
wavefront0.020.000.01

RBGL.Rcheck/examples_x64/RBGL-Ex.timings:

nameusersystemelapsed
FileDep0.650.040.70
astarSearch0.020.000.02
bandwidth0.010.000.01
bccluster0.020.000.01
bellman.ford.sp0.010.000.02
betweenness000
bfs0.010.000.02
biConnComp0.030.000.03
chrobakPayneStraightLineDrawing0.020.000.02
clusteringCoef0.010.000.01
clusteringCoefAppr0.020.000.02
coloring0.090.000.09
connectedComp0.010.000.02
dag.sp0.020.000.02
dijkstra.sp0.050.000.04
dominatorTree000
edgeConn000
edmondsMaxCardinalityMatching0.010.000.02
edmondsOptimumBranching0.020.000.02
extractPath000
floyd.warshall.all.pairs.sp0.010.000.02
gprofile0.020.000.01
graphGenerator000
highlyConnSG0.010.000.02
incrConnComp0.020.000.01
is.triangulated0.030.000.03
isKuratowskiSubgraph0.010.000.02
isStraightLineDrawing0.020.000.02
isomorphism0.020.000.01
johnson.all.pairs.sp0.010.000.02
kCliques0.020.000.01
kCores0.060.000.06
lambdaSets0.010.000.02
layout000
makeBiconnectedPlanar0.020.000.02
makeConnected0.020.000.01
makeMaximalPlanar0.030.000.03
maxClique0.000.020.02
maxFlow0.030.000.03
minCut0.010.000.02
mstree.kruskal0.040.000.03
mstree.prim0.010.000.01
ordering0.020.000.02
planarCanonicalOrdering0.010.000.01
planarFaceTraversal0.020.000.02
removeSelfLoops0.010.000.02
separates0.020.000.02
sp.between0.050.000.04
strongComp0.010.000.02
transClosure0.020.000.01
transitivity0.010.000.02
tsort0.020.000.01
wavefront0.010.000.02