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BioC 3.5: CHECK report for RBGL on veracruz2

This page was generated on 2017-10-18 14:27:24 -0400 (Wed, 18 Oct 2017).

Package 1064/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.52.0
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/RBGL
Branch: RELEASE_3_5
Last Commit: 93e8fcf
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RBGL_1.52.0.tar.gz
StartedAt: 2017-10-18 07:54:02 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 07:57:04 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 181.5 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_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RBGL.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.52.0’
* 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 shell scripts ... 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-3.5-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:57:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:61:62: warning: unused typedef 'Color' [-Wunused-local-typedef]
        typedef property_map<Graph_dd, vertex_color_t>::type Color;
                                                             ^
interfaces.cpp:99:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:98:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
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:198:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:199:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
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-3.5-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
FileDep0.7270.0230.771
astarSearch0.2440.0020.256
bandwidth0.0340.0010.036
bccluster0.0350.0010.037
bellman.ford.sp0.0670.0010.070
betweenness0.0080.0010.008
bfs0.0490.0010.051
biConnComp0.0060.0010.007
chrobakPayneStraightLineDrawing0.0090.0000.009
clusteringCoef0.0100.0010.010
clusteringCoefAppr0.0120.0010.013
coloring0.0070.0000.008
connectedComp0.0510.0020.054
dag.sp0.0380.0010.041
dijkstra.sp0.0540.0010.058
dominatorTree0.0260.0010.029
edgeConn0.0060.0010.007
edmondsMaxCardinalityMatching0.0310.0010.031
edmondsOptimumBranching0.0060.0000.007
extractPath0.0030.0010.005
floyd.warshall.all.pairs.sp0.0070.0000.007
gprofile0.0060.0010.006
graphGenerator0.0010.0000.001
highlyConnSG0.0090.0010.011
incrConnComp0.0840.0010.088
is.triangulated0.0130.0010.013
isKuratowskiSubgraph0.0080.0000.009
isStraightLineDrawing0.0090.0000.009
isomorphism0.0100.0010.012
johnson.all.pairs.sp0.0070.0000.007
kCliques0.0070.0010.007
kCores0.0900.0090.101
lambdaSets0.0180.0010.019
layout0.0020.0000.001
makeBiconnectedPlanar0.0090.0010.010
makeConnected0.0080.0000.009
makeMaximalPlanar0.0090.0010.010
maxClique0.0310.0010.034
maxFlow0.0630.0010.068
minCut0.0060.0000.007
mstree.kruskal0.0410.0010.044
mstree.prim0.0080.0010.009
ordering0.0090.0010.010
planarCanonicalOrdering0.0070.0000.008
planarFaceTraversal0.0080.0000.009
removeSelfLoops0.0090.0010.010
separates0.1210.0010.126
sp.between0.0950.0030.103
strongComp0.0260.0000.028
transClosure0.0070.0000.007
transitivity0.0050.0010.005
tsort0.0040.0010.004
wavefront0.0080.0000.008