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###
### Running command:
###
### rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RBGL_1.75.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R RBGL.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RBGL.buildbin-libdir RBGL_1.75.0.tar.gz'
>>>>>>>
* installing *source* package ‘RBGL’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bbc.cpp -o bbc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cliques.cpp -o cliques.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c clusteringCoef.cpp -o clusteringCoef.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dominatorTree.cpp -o dominatorTree.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hcs.cpp -o hcs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -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:142:60: 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: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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mincut.cpp -o mincut.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ordering.cpp -o ordering.o
ordering.cpp:182:48: warning: unused variable 'id' [-Wunused-variable]
property_map<Graph_dd, vertex_index_t>::type id = get(vertex_index, g);
^
ordering.cpp:133:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
^
ordering.cpp:176:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
^
ordering.cpp:232:47: warning: unused typedef 'Pair' [-Wunused-local-typedef]
typedef std::pair<std::size_t, std::size_t> Pair;
^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c planar.cpp -o planar.o
planar.cpp:225:30: warning: unused variable 'oi' [-Wunused-variable]
Vertex_Vec_t::iterator oi, oi_end = ordering.end();
^
planar.cpp:225:34: warning: unused variable 'oi_end' [-Wunused-variable]
Vertex_Vec_t::iterator oi, oi_end = ordering.end();
^
planar.cpp:429:32: warning: unused variable 'ki' [-Wunused-variable]
Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.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;
^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c registerSigHandlers.cpp -o registerSigHandlers.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c transitive_closure.cpp -o transitive_closure.o
In file included from transitive_closure.cpp:16:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/graph/transitive_closure.hpp:167:45: warning: 'not1<boost::detail::subscript_t<std::__1::vector<unsigned long, std::__1::allocator<unsigned long> >, unsigned long, unsigned long> >' is deprecated [-Wdeprecated-declarations]
std::not1(detail::subscript(in_a_chain)));
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/graph/transitive_closure.hpp:288:5: note: in instantiation of function template specialization 'boost::transitive_closure<R_adjacency_list<boost::directedS, double>, R_adjacency_list<boost::directedS, double>, boost::iterator_property_map<unsigned long *, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, unsigned long>, unsigned long, unsigned long &>, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, unsigned long> >' requested here
transitive_closure(g, tc, g_to_tc_map, index_map);
^
transitive_closure.cpp:29:6: note: in instantiation of function template specialization 'boost::transitive_closure<R_adjacency_list<boost::directedS, double>, R_adjacency_list<boost::directedS, double> >' requested here
transitive_closure(g, TC);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:1005:1: note: 'not1<boost::detail::subscript_t<std::__1::vector<unsigned long, std::__1::allocator<unsigned long> >, unsigned long, unsigned long> >' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX17 inline _LIBCPP_CONSTEXPR_AFTER_CXX11 _LIBCPP_INLINE_VISIBILITY
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1113:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c wavefront.cpp -o wavefront.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -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 registerSigHandlers.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-3.17-bioc/meat/RBGL.buildbin-libdir/00LOCK-RBGL/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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/4.3/Resources/lib/libgcc_s.1.dylib" "RBGL.buildbin-libdir/RBGL/libs/RBGL.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "RBGL.buildbin-libdir/RBGL/libs/RBGL.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "RBGL.buildbin-libdir/RBGL/libs/RBGL.so"
