Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.6: CHECK report for RBGL on veracruz1

This page was generated on 2017-08-16 13:38:34 -0400 (Wed, 16 Aug 2017).

Package 1081/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.53.0
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RBGL
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.53.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RBGL_1.53.0.tar.gz
StartedAt: 2017-08-16 07:22:38 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 07:25:43 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 184.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RBGL.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RBGL_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/RBGL.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.53.0’
* 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 ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-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
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c bbc.cpp -o bbc.o
In file included from bbc.cpp:3:
rbgl_trimmed_boost_1_61_0/boost/graph/bc_clustering.hpp:118:5: warning: unused typedef 'vertices_size_type' [-Wunused-local-typedef]
    vertices_size_type;
    ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c cliques.cpp -o cliques.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c clusteringCoef.cpp -o clusteringCoef.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c dominatorTree.cpp -o dominatorTree.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from edmonds_optimum_branching.cpp:3:
In file included from ./edmonds_optimum_branching.hpp:93:
./edmonds_optimum_branching_impl.hpp:522:71: warning: unused typedef 'EdgeIter' [-Wunused-local-typedef]
    typedef typename graph_traits<TEdgeListGraph>::edge_iterator      EdgeIter;
                                                                      ^
./edmonds_optimum_branching_impl.hpp:523:71: warning: unused typedef 'weight_t' [-Wunused-local-typedef]
    typedef typename property_traits<TWeightMap>::value_type          weight_t;
                                                                      ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c hcs.cpp -o hcs.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable]
            BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
                                      ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c interfaces.cpp -o interfaces.o
interfaces.cpp:61:62: warning: unused typedef 'Color' [-Wunused-local-typedef]
        typedef property_map<Graph_dd, vertex_color_t>::type Color;
                                                             ^
interfaces.cpp:57:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:98:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:99:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:143:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:142:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:199:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:198:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:226:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:225:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:253:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:252:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:295:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:320:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:360:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:361:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
16 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c minST.cpp -o minST.o
minST.cpp:14:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
minST.cpp:48:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
minST.cpp:81:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c mincut.cpp -o mincut.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ordering.cpp -o ordering.o
ordering.cpp:180:48: warning: unused variable 'id' [-Wunused-variable]
                property_map<Graph_dd, vertex_index_t>::type id = get(vertex_index, g);
                                                             ^
ordering.cpp:131:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
                typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
                                                                  ^
ordering.cpp:174:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
                typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
                                                                  ^
ordering.cpp:230:47: warning: unused typedef 'Pair' [-Wunused-local-typedef]
                typedef std::pair<std::size_t, std::size_t> Pair;
                                                            ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c planar.cpp -o planar.o
planar.cpp:225:34: warning: unused variable 'oi_end' [-Wunused-variable]
           Vertex_Vec_t::iterator oi, oi_end = ordering.end();
                                      ^
planar.cpp:429:36: warning: unused variable 'ki_end' [-Wunused-variable]
           Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.end();
                                    ^
planar.cpp:461:6: warning: unused variable 'i' [-Wunused-variable]
        int i, j = 0;
            ^
In file included from planar.cpp:5:
rbgl_trimmed_boost_1_61_0/boost/graph/planar_canonical_ordering.hpp:68:68: warning: variable 'second_vertex' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
    for(boost::tie(ai,ai_end) = adjacent_vertices(first_vertex,g); ai != ai_end; ++ai)
                                                                   ^˜˜˜˜˜˜˜˜˜˜˜
rbgl_trimmed_boost_1_61_0/boost/graph/planar_canonical_ordering.hpp:206:5: note: in instantiation of function template specialization 'boost::planar_canonical_ordering<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS>, boost::iterator_property_map<std::__1::__wrap_iter<std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > > *>, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, unsigned long>, std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > >, std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > > &>, std::__1::back_insert_iterator<std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, unsigned long> >' requested here
    planar_canonical_ordering(g, embedding, ordering, get(vertex_index,g));
    ^
planar.cpp:222:7: note: in instantiation of function template specialization 'boost::planar_canonical_ordering<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS>, boost::iterator_property_map<std::__1::__wrap_iter<std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > > *>, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, unsigned long>, std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > >, std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > > &>, std::__1::back_insert_iterator<std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > > >' requested here
           planar_canonical_ordering(g, embedding, std::back_inserter(ordering));
           ^
rbgl_trimmed_boost_1_61_0/boost/graph/planar_canonical_ordering.hpp:79:12: note: uninitialized use occurs here
    status[second_vertex] = detail::PCO_READY_TO_BE_PROCESSED;
           ^˜˜˜˜˜˜˜˜˜˜˜˜
rbgl_trimmed_boost_1_61_0/boost/graph/planar_canonical_ordering.hpp:68:68: note: remove the condition if it is always true
    for(boost::tie(ai,ai_end) = adjacent_vertices(first_vertex,g); ai != ai_end; ++ai)
                                                                   ^˜˜˜˜˜˜˜˜˜˜˜
rbgl_trimmed_boost_1_61_0/boost/graph/planar_canonical_ordering.hpp:66:27: note: initialize the variable 'second_vertex' to silence this warning
    vertex_t second_vertex;
                          ^
                           = 0
In file included from planar.cpp:3:
In file included from rbgl_trimmed_boost_1_61_0/boost/graph/boyer_myrvold_planar_test.hpp:12:
rbgl_trimmed_boost_1_61_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1530:39: warning: variable 'z' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
          for(face_itr = x_lower_itr; *face_itr != y; ++face_itr)
                                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜
rbgl_trimmed_boost_1_61_0/boost/graph/boyer_myrvold_planar_test.hpp:121:30: note: in instantiation of function template specialization 'boost::boyer_myrvold_impl<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS>, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::no_property>, unsigned long>, boost::graph::detail::store_old_handles, boost::graph::detail::no_embedding>::extract_kuratowski_subgraph<std::__1::back_insert_iterator<std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > > >, boost::adj_list_edge_property_map<boost::undirected_tag, int, int &, unsigned long, boost::property<boost::edge_index_t, int, boost::no_property>, boost::edge_index_t> >' requested here
            planarity_tester.extract_kuratowski_subgraph
                             ^
rbgl_trimmed_boost_1_61_0/boost/graph/boyer_myrvold_planar_test.hpp:253:17: note: in instantiation of function template specialization 'boost::boyer_myrvold_params::core::dispatched_boyer_myrvold<boost::parameter::aux::arg_list<const boost::parameter::aux::tagged_argument<boost::boyer_myrvold_params::tag::kuratowski_subgraph, const std::__1::back_insert_iterator<std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > > > >, boost::parameter::aux::arg_list<const boost::parameter::aux::tagged_argument<boost::boyer_myrvold_params::tag::graph, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS> >, boost::parameter::aux::empty_arg_list> > >' requested here
         return dispatched_boyer_myrvold
                ^
rbgl_trimmed_boost_1_61_0/boost/graph/boyer_myrvold_planar_test.hpp:280:40: note: in instantiation of function template specialization 'boost::boyer_myrvold_params::core::boyer_myrvold_planarity_test<boost::parameter::aux::arg_list<const boost::parameter::aux::tagged_argument<boost::boyer_myrvold_params::tag::kuratowski_subgraph, const std::__1::back_insert_iterator<std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > > > >, boost::parameter::aux::arg_list<const boost::parameter::aux::tagged_argument<boost::boyer_myrvold_params::tag::graph, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS> >, boost::parameter::aux::empty_arg_list> > >' requested here
    return boyer_myrvold_params::core::boyer_myrvold_planarity_test
                                       ^
planar.cpp:414:9: note: in instantiation of function template specialization 'boost::boyer_myrvold_planarity_test<boost::parameter::aux::tagged_argument<boost::boyer_myrvold_params::tag::graph, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::property<boost::edge_index_t, int, boost::no_property>, boost::no_property, boost::listS> >, boost::parameter::aux::tagged_argument<boost::boyer_myrvold_params::tag::kuratowski_subgraph, const std::__1::back_insert_iterator<std::__1::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long>, std::__1::allocator<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned long> > > > > >' requested here
        if ( boyer_myrvold_planarity_test(
             ^
rbgl_trimmed_boost_1_61_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1545:33: note: uninitialized use occurs here
          if (externally_active(z,v))
                                ^
rbgl_trimmed_boost_1_61_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1530:39: note: remove the condition if it is always true
          for(face_itr = x_lower_itr; *face_itr != y; ++face_itr)
                                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜
rbgl_trimmed_boost_1_61_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1237:17: note: initialize the variable 'z' to silence this warning
      vertex_t z; 
                ^
                 = 0
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp:17:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
shortestPath.cpp:136:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
shortestPath.cpp:177:81: warning: unused typedef 'Graph' [-Wunused-local-typedef]
        property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
                                                                                ^
shortestPath.cpp:180:39: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef std::pair < int, int >Edge;
                                      ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sna.cpp -o sna.o
sna.cpp:161:9: warning: unused variable 'res_cap' [-Wunused-variable]
        res_cap = get(edge_residual_capacity, flow_g);
        ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c transitive_closure.cpp -o transitive_closure.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fPIC  -Wall -g -O2  -c wavefront.cpp -o wavefront.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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
FileDep0.6440.0180.671
astarSearch0.2430.0010.245
bandwidth0.0380.0010.038
bccluster0.0320.0010.033
bellman.ford.sp0.0630.0000.070
betweenness0.0080.0000.009
bfs0.0460.0010.049
biConnComp0.0070.0010.008
chrobakPayneStraightLineDrawing0.0080.0000.009
clusteringCoef0.0090.0000.010
clusteringCoefAppr0.0110.0000.011
coloring0.0050.0000.006
connectedComp0.0490.0010.050
dag.sp0.0360.0010.036
dijkstra.sp0.0530.0010.058
dominatorTree0.0240.0010.025
edgeConn0.0040.0000.005
edmondsMaxCardinalityMatching0.0970.0000.098
edmondsOptimumBranching0.0060.0010.007
extractPath0.0030.0010.004
floyd.warshall.all.pairs.sp0.0060.0010.007
gprofile0.0060.0000.007
graphGenerator0.0010.0000.001
highlyConnSG0.0090.0000.009
incrConnComp0.0070.0010.008
is.triangulated0.0120.0010.013
isKuratowskiSubgraph0.0080.0010.009
isStraightLineDrawing0.0090.0010.010
isomorphism0.0110.0020.012
johnson.all.pairs.sp0.0070.0010.008
kCliques0.0070.0010.008
kCores0.0810.0030.091
lambdaSets0.0190.0000.019
layout0.0010.0000.010
makeBiconnectedPlanar0.0090.0000.009
makeConnected0.010.000.01
makeMaximalPlanar0.0090.0000.010
maxClique0.0290.0000.029
maxFlow0.0560.0000.057
minCut0.0060.0000.006
mstree.kruskal0.0380.0010.039
mstree.prim0.0070.0010.007
ordering0.0070.0000.008
planarCanonicalOrdering0.0070.0010.008
planarFaceTraversal0.0070.0010.008
removeSelfLoops0.0110.0000.011
separates0.1260.0010.127
sp.between0.0920.0020.100
strongComp0.0280.0010.028
transClosure0.0090.0000.012
transitivity0.0040.0010.004
tsort0.0050.0010.005
wavefront0.0070.0010.007