##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RBGL_1.58.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R RBGL.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RBGL.buildbin-libdir RBGL_1.58.2.tar.gz'
>>>>>>>
* installing *source* package ‘RBGL’ ...
removing exploded boost header source...
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 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: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: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: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:225:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:226:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp:252:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:253:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
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: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 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-3.8-bioc/meat/RBGL.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR RBGL.buildbin-libdir/RBGL/libs//RBGL.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
