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BioC 3.4: CHECK report for RBGL on malbec1

This page was generated on 2017-04-15 16:08:47 -0400 (Sat, 15 Apr 2017).

Package 1001/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.50.0
Bioconductor Package Maintainer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/RBGL
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.50.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.50.0.tar.gz
StartedAt: 2017-04-15 00:43:31 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:45:39 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 127.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RBGL.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RBGL.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.50.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs       24.9Mb
    old_boost   1.9Mb
* 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
* 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 ... 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 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 ... WARNING
File ‘RBGL/libs/RBGL.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Objects: ‘ordering.o’, ‘planar.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/RBGL.Rcheck/00check.log’
for details.

RBGL.Rcheck/00install.out:

* installing *source* package ‘RBGL’ ...
found  rbgl_trimmed_boost_1_61_0  header sources and tar archive;
 using what is there.
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c bbc.cpp -o bbc.o
In file included from bbc.cpp:3:0:
rbgl_trimmed_boost_1_61_0/boost/graph/bc_clustering.hpp: In function ‘void boost::betweenness_centrality_clustering(MutableGraph&, Done, EdgeCentralityMap, VertexIndexMap)’:
rbgl_trimmed_boost_1_61_0/boost/graph/bc_clustering.hpp:118:5: warning: typedef ‘vertices_size_type’ locally defined but not used [-Wunused-local-typedefs]
     vertices_size_type;
     ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c cliques.cpp -o cliques.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -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 [-Wmaybe-uninitialized]
         Graph_ud::vertex_descriptor v, u, w=Graph_ud::null_vertex();
                                        ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c dominatorTree.cpp -o dominatorTree.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from edmonds_optimum_branching.hpp:93:0,
                 from edmonds_optimum_branching.cpp:3:
edmonds_optimum_branching_impl.hpp: In function ‘void edmonds_optimum_branching(TEdgeListGraph&, TVertexIndexMap, TWeightMap, TInputIterator, TInputIterator, TOutputIterator)’:
edmonds_optimum_branching_impl.hpp:522:71: warning: typedef ‘EdgeIter’ locally defined but not used [-Wunused-local-typedefs]
     typedef typename graph_traits<TEdgeListGraph>::edge_iterator      EdgeIter;
                                                                       ^
edmonds_optimum_branching_impl.hpp:523:71: warning: typedef ‘weight_t’ locally defined but not used [-Wunused-local-typedefs]
     typedef typename property_traits<TWeightMap>::value_type          weight_t;
                                                                       ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c hcs.cpp -o hcs.o
In file included from mincut.hpp:4:0,
                 from hcs.cpp:2:
rbgl_trimmed_boost_1_61_0/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >; typename boost::graph_traits<G>::edges_size_type = long unsigned int]’:
rbgl_trimmed_boost_1_61_0/boost/graph/edge_connectivity.hpp:32:42: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       typename Traits::vertex_descriptor p;
                                          ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c incrConnComp.cpp -o incrConnComp.o
In file included from incrConnComp.cpp:2:0:
incrConnComp.cpp: In function ‘SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)’:
incrConnComp.cpp:74:32: warning: unused variable ‘child_index’ [-Wunused-variable]
      BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
                                ^
rbgl_trimmed_boost_1_61_0/boost/foreach.hpp:1107:14: note: in definition of macro ‘BOOST_FOREACH’
         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c interfaces.cpp -o interfaces.o
interfaces.cpp: In function ‘SEXPREC* BGL_tsort_D(SEXP, SEXP, SEXP)’:
interfaces.cpp:57:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^
interfaces.cpp:61:62: warning: typedef ‘Color’ locally defined but not used [-Wunused-local-typedefs]
         typedef property_map<Graph_dd, vertex_color_t>::type Color;
                                                              ^
interfaces.cpp: In function ‘SEXPREC* BGL_bfs_D(SEXP, SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:98:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^
interfaces.cpp:99:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                              ^
interfaces.cpp: In function ‘SEXPREC* BGL_dfs_D(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:142:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^
interfaces.cpp:143:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                              ^
interfaces.cpp: In function ‘SEXPREC* BGL_connected_components_U(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:198:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^
interfaces.cpp:199:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                              ^
interfaces.cpp: In function ‘SEXPREC* BGL_strong_components_D(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:225:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^
interfaces.cpp:226:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                              ^
interfaces.cpp: In function ‘SEXPREC* BGL_biconnected_components_U(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:252:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^
interfaces.cpp:253:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                              ^
interfaces.cpp: In function ‘SEXPREC* BGL_articulation_points_U(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:295:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^
interfaces.cpp: In function ‘SEXPREC* BGL_edge_connectivity_U(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:320:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                              ^
interfaces.cpp: In function ‘SEXPREC* BGL_sequential_vertex_coloring(SEXP, SEXP, SEXP)’:
interfaces.cpp:360:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^
interfaces.cpp:361:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                              ^
In file included from interfaces.cpp:7:0:
rbgl_trimmed_boost_1_61_0/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >; typename boost::graph_traits<G>::degree_size_type = long unsigned int]’:
rbgl_trimmed_boost_1_61_0/boost/graph/edge_connectivity.hpp:32:42: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       typename Traits::vertex_descriptor p;
                                          ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c minST.cpp -o minST.o
minST.cpp: In function ‘SEXPREC* BGL_KMST_D(SEXP, SEXP, SEXP, SEXP)’:
minST.cpp:14:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                              ^
minST.cpp: In function ‘SEXPREC* BGL_KMST_U(SEXP, SEXP, SEXP, SEXP)’:
minST.cpp:48:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                              ^
minST.cpp: In function ‘SEXPREC* BGL_PRIM_U(SEXP, SEXP, SEXP, SEXP)’:
minST.cpp:81:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from minST.cpp:1:
rbgl_trimmed_boost_1_61_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_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
In file included from minST.cpp:2:0:
rbgl_trimmed_boost_1_61_0/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)& ei +48)’ was declared here
       typename graph_traits<Graph>::edge_iterator ei, eiend;
                                                   ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:41:0,
                 from RBGL.hpp:37,
                 from minST.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/edge.hpp:25:34: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<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 [-Wmaybe-uninitialized]
         : m_source(s), m_target(d) { }
                                  ^
In file included from minST.cpp:2:0:
rbgl_trimmed_boost_1_61_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::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<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
       typename graph_traits<Graph>::edge_iterator ei, eiend;
                                                   ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c mincut.cpp -o mincut.o
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from mincut.cpp:1:
rbgl_trimmed_boost_1_61_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_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
mincut.cpp:99:19: note: ‘*((void*)& ei +48)’ was declared here
     edge_iterator ei, e_end;
                   ^
mincut.cpp:103:54: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<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::stored_edge_property<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::stored_edge_property<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 [-Wmaybe-uninitialized]
             INTEGER(eList)[i++] = source(*ei, flow_g);
                                                      ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246:0,
                 from RBGL.hpp:37,
                 from mincut.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:152:62: warning: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<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::stored_edge_property<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::stored_edge_property<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 [-Wmaybe-uninitialized]
                               &(*this->base()).get_property());
                                                              ^
mincut.cpp:99:19: note: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<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::stored_edge_property<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::stored_edge_property<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
     edge_iterator ei, e_end;
                   ^
In file included from mincut.hpp:4:0,
                 from mincut.cpp:2:
rbgl_trimmed_boost_1_61_0/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >; typename boost::graph_traits<G>::edges_size_type = long unsigned int]’:
rbgl_trimmed_boost_1_61_0/boost/graph/edge_connectivity.hpp:32:42: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       typename Traits::vertex_descriptor p;
                                          ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c ordering.cpp -o ordering.o
ordering.cpp: In function ‘SEXPREC* BGL_min_degree_ordering(SEXP, SEXP, SEXP, SEXP)’:
ordering.cpp:131:53: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
   typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
                                                     ^
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]
   property_map<Graph_dd, vertex_index_t>::type id = get(vertex_index, g);
                                                ^
ordering.cpp:174:53: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
   typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
                                                     ^
ordering.cpp: In function ‘SEXPREC* BGL_sloan_ordering(SEXP, SEXP, SEXP, SEXP, SEXP)’:
ordering.cpp:230:47: warning: typedef ‘Pair’ locally defined but not used [-Wunused-local-typedefs]
   typedef std::pair<std::size_t, std::size_t> Pair;
                                               ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c planar.cpp -o planar.o
planar.cpp: In function ‘SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)’:
planar.cpp:161:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
            for ( int i = 0; i < v_vis.f_vis.size(); i++ )
                               ^
planar.cpp:165:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for ( int j = 0; j < v_vis.f_vis[i].size(); j++ )
                                    ^
planar.cpp: In function ‘SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)’:
planar.cpp:256:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < ordering.size(); i++ )
                        ^
planar.cpp: In function ‘SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)’:
planar.cpp:369:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int i = 0, j = 0; i < num_vertices(g); i++ )
                            ^
planar.cpp: In function ‘SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)’:
planar.cpp:461:6: warning: unused variable ‘i’ [-Wunused-variable]
  int i, j = 0;
      ^
In file included from planar.cpp:5:0:
rbgl_trimmed_boost_1_61_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_61_0/boost/graph/planar_canonical_ordering.hpp:152:22: warning: ‘second_vertex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                      !(first_vertex == x && second_vertex == u)
                      ^
In file included from planar.cpp:6:0:
rbgl_trimmed_boost_1_61_0/boost/graph/chrobak_payne_drawing.hpp: In function ‘void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, 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> >; ForwardIterator = __gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >; GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<coord_t*, std::vector<coord_t> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, 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_61_0/boost/graph/chrobak_payne_drawing.hpp:217:22: warning: ‘next_to_rightmost’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             vertex_t next_to_rightmost;
                      ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/boyer_myrvold_planar_test.hpp:12:0,
                 from planar.cpp:3:
rbgl_trimmed_boost_1_61_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function ‘void boost::boyer_myrvold_impl<Graph, VertexIndexMap, StoreOldHandlesPolicy, StoreEmbeddingPolicy>::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >; EdgeIndexMap = boost::adj_list_edge_property_map<boost::undirected_tag, int, int&, long unsigned int, boost::property<boost::edge_index_t, int>, boost::edge_index_t>; Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>; StoreOldHandlesPolicy = boost::graph::detail::store_old_handles; StoreEmbeddingPolicy = boost::graph::detail::no_embedding]’:
rbgl_trimmed_boost_1_61_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1237:16: warning: ‘z’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       vertex_t z; 
                ^
rbgl_trimmed_boost_1_61_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1406:7: warning: ‘bicomp_root’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (bicomp_root != v)
       ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/depth_first_search.hpp:21:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/boyer_myrvold_planar_test.hpp:12,
                 from planar.cpp:3:
rbgl_trimmed_boost_1_61_0/boost/graph/named_function_params.hpp: In static member function ‘static bool boost::maximum_cardinality_matching_verifier<Graph, MateMap, VertexIndexMap>::verify_matching(const Graph&, MateMap, VertexIndexMap) [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_61_0/boost/graph/named_function_params.hpp:124:64: warning: ‘*((void*)& occ +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     bgl_named_params(T v, const Base& b) : m_value(v), m_base(b) { }
                                                                ^
In file included from planar.cpp:11:0:
rbgl_trimmed_boost_1_61_0/boost/graph/max_cardinality_matching.hpp:820:48: note: ‘*((void*)& occ +16)’ was declared here
       detail::odd_components_counter<v_size_t> occ(num_odd_components);
                                                ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp: In function ‘SEXPREC* BGL_dijkstra_shortest_paths_D(SEXP, SEXP, SEXP, SEXP, SEXP)’:
shortestPath.cpp:17:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^
shortestPath.cpp: In function ‘SEXPREC* BGL_dag_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)’:
shortestPath.cpp:136:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^
shortestPath.cpp: In function ‘SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXP, SEXP, SEXP, SEXP)’:
shortestPath.cpp:177:81: warning: typedef ‘Graph’ locally defined but not used [-Wunused-local-typedefs]
         property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
                                                                                 ^
shortestPath.cpp:180:39: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef std::pair < int, int >Edge;
                                       ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>; Size = long unsigned int; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>, boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
rbgl_trimmed_boost_1_61_0/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)& i +48)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::floyd_warshall_all_pairs_shortest_paths(const VertexAndEdgeListGraph&, DistanceMatrix&, const WeightMap&, const BinaryPredicate&, const BinaryFunction&, const Infinity&, const Zero&) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>; DistanceMatrix = Basic2DMatrix<double>; WeightMap = 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>; BinaryPredicate = std::less<double>; BinaryFunction = boost::closed_plus<double>; Infinity = double; Zero = double]’:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& first +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
In file included from shortestPath.cpp:7:0:
rbgl_trimmed_boost_1_61_0/boost/graph/floyd_warshall_shortest.hpp:111:66: note: ‘*((void*)& first +48)’ was declared here
     typename graph_traits<VertexAndEdgeListGraph>::edge_iterator first, last;
                                                                  ^
rbgl_trimmed_boost_1_61_0/boost/graph/floyd_warshall_shortest.hpp:125:12: warning: ‘*((void*)(& first)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<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 [-Wmaybe-uninitialized]
       if (d[source(*first, g)][target(*first, g)] != inf) {
            ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246:0,
                 from RBGL.hpp:37,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:152:62: warning: ‘*((void*)(& first)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                               &(*this->base()).get_property());
                                                              ^
In file included from shortestPath.cpp:7:0:
rbgl_trimmed_boost_1_61_0/boost/graph/floyd_warshall_shortest.hpp:111:66: note: ‘*((void*)(& first)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ was declared here
     typename graph_traits<VertexAndEdgeListGraph>::edge_iterator first, last;
                                                                  ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::no_property, boost::property<boost::edge_weight_t, double, boost::no_property> >; Size = int; WeightMap = 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>; PredecessorMap = long unsigned int*; DistanceMap = double*; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
rbgl_trimmed_boost_1_61_0/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)& i +48)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
In file included from RBGL.hpp:16:0,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/property_map/property_map.hpp:127:65: warning: ‘*((void*)(& i)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<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 [-Wmaybe-uninitialized]
   inline const T& get(const T* pa, std::ptrdiff_t k) { return pa[k]; }
                                                                 ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
rbgl_trimmed_boost_1_61_0/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)(& i)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<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
     typename GTraits::edge_iterator i, end;
                                     ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246:0,
                 from RBGL.hpp:37,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:152:62: warning: ‘*((void*)(& i)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                               &(*this->base()).get_property());
                                                              ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
rbgl_trimmed_boost_1_61_0/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)(& i)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_bellman_ford_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)’:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
shortestPath.cpp:101:50: note: ‘*((void*)& ei +48)’ was declared here
         graph_traits< EdgeGraph >::edge_iterator ei, ei_end;
                                                  ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.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_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
In file included from shortestPath.cpp:4:0:
rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)& e +48)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
In file included from rbgl_trimmed_boost_1_61_0/boost/shared_array.hpp:17:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/detail/d_ary_heap.hpp:20,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/named_function_params.hpp:24,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/dijkstra_shortest_paths.hpp:20,
                 from shortestPath.cpp:3:
rbgl_trimmed_boost_1_61_0/boost/smart_ptr/shared_array.hpp:200:18: warning: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > > > > >, 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 [-Wmaybe-uninitialized]
         return px[i];
                  ^
In file included from shortestPath.cpp:4:0:
rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from shortestPath.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
In file included from shortestPath.cpp:4:0:
rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:84:39: note: ‘*((void*)& e +48)’ was declared here
       typename Traits1::edge_iterator e, e_end;
                                       ^
rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:87:37: warning: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<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 [-Wmaybe-uninitialized]
         boost::tie(e2, z) = add_edge(get(id1, source(*e, g1)) + 1, 
                                     ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -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]
         res_cap = get(edge_residual_capacity, flow_g);
         ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from sna.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>; Size = long unsigned int; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from sna.cpp:3:
rbgl_trimmed_boost_1_61_0/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)& i +48)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from RBGL.hpp:37,
                 from sna.cpp:1:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.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_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
In file included from sna.cpp:3:0:
rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)& e +48)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
In file included from rbgl_trimmed_boost_1_61_0/boost/property_map/shared_array_property_map.hpp:13:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from sna.cpp:3:
rbgl_trimmed_boost_1_61_0/boost/smart_ptr/shared_array.hpp:200:18: warning: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_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 [-Wmaybe-uninitialized]
         return px[i];
                  ^
In file included from sna.cpp:3:0:
rbgl_trimmed_boost_1_61_0/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_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
     typename Traits2::edge_iterator e, e_end;
                                     ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c transitive_closure.cpp -o transitive_closure.o
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/detail/adjacency_list.hpp:34:0,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/adjacency_list.hpp:246,
                 from rbgl_trimmed_boost_1_61_0/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_transitive_closure_D(SEXP, SEXP, SEXP)’:
rbgl_trimmed_boost_1_61_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) 
         ^
transitive_closure.cpp:43:33: note: ‘*((void*)& ei +48)’ was declared here
         Graph_dd::edge_iterator ei, e_end;
                                 ^
transitive_closure.cpp:46:50: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<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 [-Wmaybe-uninitialized]
             INTEGER(eList)[i++] = source(*ei, TC);
                                                  ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0 -I/usr/local/include    -fpic  -g -O2  -Wall -c wavefront.cpp -o wavefront.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/RBGL.Rcheck/RBGL/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RBGL)

RBGL.Rcheck/RBGL-Ex.timings:

nameusersystemelapsed
FileDep0.3040.0080.311
astarSearch0.0040.0000.004
bandwidth0.0080.0000.012
bccluster0.0040.0000.008
bellman.ford.sp0.0040.0000.006
betweenness0.0080.0000.006
bfs0.0120.0000.012
biConnComp0.0040.0000.005
chrobakPayneStraightLineDrawing0.0040.0000.007
clusteringCoef0.0080.0000.007
clusteringCoefAppr0.0080.0000.007
coloring0.0120.0040.015
connectedComp0.0160.0000.031
dag.sp0.0120.0000.009
dijkstra.sp0.0280.0000.027
dominatorTree0.0080.0000.007
edgeConn0.0080.0000.008
edmondsMaxCardinalityMatching0.0160.0000.016
edmondsOptimumBranching0.0120.0000.011
extractPath0.0040.0000.005
floyd.warshall.all.pairs.sp0.0080.0000.009
gprofile0.0080.0000.007
graphGenerator0.0040.0000.001
highlyConnSG0.0120.0000.010
incrConnComp0.0080.0000.009
is.triangulated0.0160.0000.014
isKuratowskiSubgraph0.0080.0000.008
isStraightLineDrawing0.0040.0000.007
isomorphism0.0040.0000.007
johnson.all.pairs.sp0.0040.0000.006
kCliques0.0080.0000.005
kCores0.0200.0040.026
lambdaSets0.0040.0000.006
layout000
makeBiconnectedPlanar0.0080.0000.008
makeConnected0.0040.0000.007
makeMaximalPlanar0.0080.0000.007
maxClique0.0120.0000.009
maxFlow0.0080.0000.008
minCut0.0040.0000.004
mstree.kruskal0.0200.0000.017
mstree.prim0.0040.0000.005
ordering0.0080.0000.007
planarCanonicalOrdering0.0040.0000.005
planarFaceTraversal0.0040.0000.006
removeSelfLoops0.0080.0000.007
separates0.0080.0000.008
sp.between0.0760.0000.076
strongComp0.0080.0000.008
transClosure0.0040.0000.006
transitivity0.0080.0000.004
tsort0.0040.0000.003
wavefront0.0000.0040.005