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This page was generated on 2021-06-18 14:06:56 -0400 (Fri, 18 Jun 2021).

BUILD BIN results for RBGL on machv2

To the developers/maintainers of the RBGL package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RBGL.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1507/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.68.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/RBGL
Branch: RELEASE_3_13
Last Commit: 9433738
Last Changed Date: 2021-05-19 11:33:37 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RBGL
Version: 1.68.0
Command: rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RBGL_1.68.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R RBGL.buildbin-libdir
StartedAt: 2021-06-18 03:01:36 -0400 (Fri, 18 Jun 2021)
EndedAt: 2021-06-18 03:03:59 -0400 (Fri, 18 Jun 2021)
EllapsedTime: 142.7 seconds
RetCode: 0
Status:   OK  
PackageFile: RBGL_1.68.0.tgz
PackageFileSize: 2.627 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RBGL_1.68.0.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_1.68.0.tar.gz'
>>>>>>> 

* installing *source* package ‘RBGL’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bbc.cpp -o bbc.o
In file included from bbc.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cliques.cpp -o cliques.o
In file included from cliques.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c clusteringCoef.cpp -o clusteringCoef.o
In file included from clusteringCoef.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c dominatorTree.cpp -o dominatorTree.o
In file included from dominatorTree.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/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:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
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;
                                                                      ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c hcs.cpp -o hcs.o
In file included from hcs.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c incrConnComp.cpp -o incrConnComp.o
In file included from incrConnComp.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable]
            BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
                                      ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c interfaces.cpp -o interfaces.o
In file included from interfaces.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
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: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: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: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: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;
                                                           ^
17 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c minST.cpp -o minST.o
In file included from minST.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
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;
                                                           ^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c mincut.cpp -o mincut.o
In file included from mincut.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ordering.cpp -o ordering.o
In file included from ordering.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from ordering.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/cuthill_mckee_ordering.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/sparse_ordering.hpp:24:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages]
BOOST_PRAGMA_MESSAGE(
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:112:2: note: expanded from here
 message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " "<boost/bind/bind.hpp> + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.")
 ^
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;
                                                            ^
6 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c planar.cpp -o planar.o
In file included from planar.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
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;
            ^
6 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c registerSigHandlers.cpp -o registerSigHandlers.o
In file included from registerSigHandlers.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c shortestPath.cpp -o shortestPath.o
In file included from shortestPath.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
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;
                                      ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sna.cpp -o sna.o
In file included from sna.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
sna.cpp:161:9: warning: unused variable 'res_cap' [-Wunused-variable]
        res_cap = get(edge_residual_capacity, flow_g);
        ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/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:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/transitive_closure.hpp:16:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages]
BOOST_PRAGMA_MESSAGE(
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:419:2: note: expanded from here
 message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " "<boost/bind/bind.hpp> + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.")
 ^
In file included from transitive_closure.cpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/transitive_closure.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/strong_components.hpp:267:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/transpose_graph.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/reverse_graph.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:175:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c wavefront.cpp -o wavefront.o
In file included from wavefront.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:129:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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-3.13-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/4.1/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/4.1/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/4.1/Resources/lib/libquadmath.0.dylib" "RBGL.buildbin-libdir/RBGL/libs/RBGL.so"