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CHECK report for RBGL on merida2

This page was generated on 2018-10-17 08:46:09 -0400 (Wed, 17 Oct 2018).

Package 1185/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.56.0
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RBGL
Branch: RELEASE_3_7
Last Commit: a1fa9d8
Last Changed Date: 2018-04-30 10:34:58 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.56.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RBGL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RBGL_1.56.0.tar.gz
StartedAt: 2018-10-16 23:32:06 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:32:55 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 49.2 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RBGL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RBGL_1.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RBGL.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.56.0’
* 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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RBGL/libs/RBGL.so’:
  Found ‘_abort’, possibly from ‘abort’ (C)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/RBGL.Rcheck/00check.log’
for details.

Installation output

RBGL.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RBGL
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RBGL’ ...
untarring boost include tree...
** 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:94:
./edmonds_optimum_branching_impl.hpp:520:71: warning: unused typedef 'EdgeIter' [-Wunused-local-typedef]
    typedef typename graph_traits<TEdgeListGraph>::edge_iterator      EdgeIter;
                                                                      ^
./edmonds_optimum_branching_impl.hpp:521:71: 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:361:62: 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;
                                                           ^
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:180:39: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef std::pair < int, int >Edge;
                                      ^
shortestPath.cpp:177:81: warning: unused typedef 'Graph' [-Wunused-local-typedef]
        property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
                                                                                ^
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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RBGL/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RBGL)

Tests output

RBGL.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("RBGL")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min



RUNIT TEST PROTOCOL -- Tue Oct 16 23:32:48 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RBGL RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.836   0.087   0.895

Example timings

RBGL.Rcheck/RBGL-Ex.timings

nameusersystemelapsed
FileDep0.4350.0310.467
astarSearch0.0680.0000.070
bandwidth0.0150.0010.016
bccluster0.0080.0000.009
bellman.ford.sp0.0420.0000.044
betweenness0.0090.0010.010
bfs0.0130.0000.015
biConnComp0.0090.0000.010
boyerMyrvoldPlanarityTest0.0110.0000.011
chrobakPayneStraightLineDrawing0.0430.0020.044
clusteringCoef0.0120.0000.012
clusteringCoefAppr0.0090.0000.010
coloring0.0080.0010.009
connectedComp0.0160.0010.017
dag.sp0.0110.0010.012
dijkstra.sp0.0210.0020.022
dominatorTree0.0080.0010.008
edgeConn0.0080.0000.008
edmondsMaxCardinalityMatching0.0200.0010.027
edmondsOptimumBranching0.010.000.01
extractPath0.0050.0010.006
floyd.warshall.all.pairs.sp0.0100.0010.010
gprofile0.0070.0010.008
graphGenerator0.0010.0000.001
highlyConnSG0.0100.0010.011
incrConnComp0.0070.0000.007
is.triangulated0.0140.0000.015
isKuratowskiSubgraph0.0080.0000.009
isStraightLineDrawing0.0080.0010.008
isomorphism0.0080.0000.009
johnson.all.pairs.sp0.0050.0010.006
kCliques0.0070.0010.008
kCores0.0360.0010.038
lambdaSets0.0090.0010.009
layout0.0010.0010.002
makeBiconnectedPlanar0.0110.0000.011
makeConnected0.0080.0010.008
makeMaximalPlanar0.0080.0000.008
maxClique0.0100.0000.011
maxFlow0.0090.0010.010
minCut0.0060.0000.006
mstree.kruskal0.0220.0010.024
mstree.prim0.0080.0000.008
ordering0.0100.0010.010
planarCanonicalOrdering0.0100.0010.012
planarFaceTraversal0.0070.0000.008
removeSelfLoops0.0120.0000.013
separates0.0130.0010.014
sp.between0.0280.0020.029
strongComp0.0150.0010.016
transClosure0.0070.0000.008
transitivity0.0050.0000.006
tsort0.0050.0010.005
wavefront0.0140.0000.015