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CHECK report for RBGL on merida1

This page was generated on 2021-05-06 12:36:18 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RBGL package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1457/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.66.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RBGL
Branch: RELEASE_3_12
Last Commit: bf0c111
Last Changed Date: 2020-10-27 10:22:59 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.66.0
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_1.66.0.tar.gz
StartedAt: 2021-05-06 05:11:14 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:12:00 -0400 (Thu, 06 May 2021)
EllapsedTime: 46.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/RBGL.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.66.0’
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/RBGL.Rcheck/00check.log’
for details.

Installation output

RBGL.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘RBGL’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from bbc.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::no_property, boost::listS>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
bbc.cpp:18:9: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<boost::vertex_centrality_t, double, boost::no_property> >, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double, boost::no_property> >, boost::no_property, boost::listS> >' requested here
typedef graph_traits<BCGraph>::edge_descriptor Edge;
        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from cliques.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'R_adjacency_list<boost::undirectedS, double>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
cliques.cpp:23:39: note: in instantiation of template class 'boost::graph_traits<R_adjacency_list<boost::undirectedS, double> >' requested here
    static bool isClique(Graph_ud& g, graph_traits < Graph_ud >::vertex_descriptor v)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from clusteringCoef.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
clusteringCoef.cpp:20:9: note: in instantiation of template class 'R_adjacency_list<boost::undirectedS, double>' requested here
        Graph_ud::vertex_iterator vi, v_end;
        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from dominatorTree.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
dominatorTree.cpp:19:18: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::listS, boost::bidirectionalS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::no_property, boost::no_property, boost::listS>' requested here
         VEGraph g(NV);
                 ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
edmonds_optimum_branching.cpp:14:18: note: in instantiation of template class 'R_adjacency_list<boost::directedS, double>' requested here
        Graph_dd g(num_verts_in, num_edges_in, R_edges_in, R_weights_in);
                 ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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;
                                                                      ^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from hcs.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'R_adjacency_list<boost::undirectedS, double>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
hcs.cpp:12:9: note: in instantiation of template class 'boost::graph_traits<R_adjacency_list<boost::undirectedS, double> >' requested here
typedef graph_traits < Graph_ud >::vertex_descriptor vertex_descriptor;
        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from incrConnComp.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'R_adjacency_list<boost::undirectedS, double>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
incrConnComp.cpp:11:17: note: in instantiation of template class 'boost::graph_traits<R_adjacency_list<boost::undirectedS, double> >' requested here
        typedef graph_traits<Graph_ud>::vertex_descriptor Vertex;
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable]
            BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
                                      ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from interfaces.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'R_adjacency_list<boost::directedS, double>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
interfaces.cpp:57:17: note: in instantiation of template class 'boost::graph_traits<R_adjacency_list<boost::directedS, double> >' requested here
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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: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: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: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:360:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:361:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
18 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from minST.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'R_adjacency_list<boost::directedS, double>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
minST.cpp:13:17: note: in instantiation of template class 'boost::graph_traits<R_adjacency_list<boost::directedS, double> >' requested here
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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;
                                                           ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from mincut.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::no_property, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, unsigned long>, boost::no_property> > >, boost::no_property, boost::listS>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
mincut.cpp:24:13: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::no_property, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, unsigned long>, boost::no_property> > >, boost::no_property, boost::listS> >' requested here
    typedef graph_traits<FlowGraph>::edge_iterator   edge_iterator;
            ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: 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/4.0/Resources/library/BH/include/boost/graph/cuthill_mckee_ordering.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/sparse_ordering.hpp:24:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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>:45:2: 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 ordering.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
ordering.cpp:36:11: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::listS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::no_property>, boost::no_property, boost::no_property, boost::listS>' requested here
                VEGraph g1(NV1), g2(NV2);
                        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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;
                                                            ^
7 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from planar.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/is_kuratowski_subgraph.hpp:114:30: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::no_property, boost::no_property, boost::no_property, boost::listS>' requested here
    static small_graph_t K_5(detail::make_K_5< small_graph_t >());
                             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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;
            ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from shortestPath.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'R_adjacency_list<boost::directedS, double>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
shortestPath.cpp:17:17: note: in instantiation of template class 'boost::graph_traits<R_adjacency_list<boost::directedS, double> >' requested here
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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;
                                      ^
6 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from sna.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
sna.cpp:100:18: note: in instantiation of template class 'R_adjacency_list<boost::undirectedS, double>' requested here
        Graph_ud g(num_verts_in, num_edges_in, R_edges_in, R_weights_in);
                 ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
sna.cpp:161:9: warning: unused variable 'res_cap' [-Wunused-variable]
        res_cap = get(edge_residual_capacity, flow_g);
        ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/transitive_closure.hpp:16:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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>:296:2: 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/4.0/Resources/library/BH/include/boost/graph/transitive_closure.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/strong_components.hpp:267:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/transpose_graph.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/reverse_graph.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:144:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from transitive_closure.cpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/transitive_closure.hpp:21:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/transitive_closure.hpp:93:10: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::no_property, boost::no_property, boost::no_property, boost::listS>' requested here
    CG_t CG(num_scc);
         ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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>:94:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from wavefront.cpp:1:
In file included from ./RBGL.hpp:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
./RBGL.hpp:46:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::no_property, boost::listS>' requested here
            : public boost::adjacency_list<boost::vecS, boost::vecS, DirectedS,
                     ^
wavefront.cpp:13:12: note: in instantiation of template class 'R_adjacency_list<boost::undirectedS, double>' requested here
                Graph_ud g(num_verts_in, num_edges_in, R_edges_in);
                         ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/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
   ‘RBGL.Rnw’ 
** 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)

Tests output

RBGL.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min



RUNIT TEST PROTOCOL -- Thu May  6 05:11:51 2021 
*********************************************** 
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 
  0.938   0.096   1.013

Example timings

RBGL.Rcheck/RBGL-Ex.timings

nameusersystemelapsed
FileDep0.5340.0330.569
astarSearch0.0540.0000.054
bandwidth0.0120.0010.013
bellman.ford.sp0.0440.0010.046
bfs0.0120.0010.014
biConnComp0.0060.0010.007
boyerMyrvoldPlanarityTest0.0080.0010.010
chrobakPayneStraightLineDrawing0.0450.0030.048
clusteringCoef0.0060.0010.007
clusteringCoefAppr0.0090.0010.011
coloring0.0050.0010.006
connectedComp0.0140.0020.017
dag.sp0.0090.0020.011
dijkstra.sp0.0160.0020.018
dominatorTree0.0040.0010.005
edgeConn0.0050.0010.005
edmondsMaxCardinalityMatching0.0100.0020.011
edmondsOptimumBranching0.0080.0010.010
extractPath0.0030.0010.004
floyd.warshall.all.pairs.sp0.0050.0010.007
gprofile0.0060.0000.007
graphGenerator0.0000.0000.001
highlyConnSG0.0090.0000.010
incrConnComp0.0080.0010.010
is.triangulated0.0130.0010.013
isKuratowskiSubgraph0.0070.0020.009
isStraightLineDrawing0.0060.0010.008
isomorphism0.0080.0010.009
johnson.all.pairs.sp0.0050.0010.007
kCliques0.0060.0010.006
kCores0.0390.0020.040
lambdaSets0.0060.0010.008
layout0.0000.0010.000
makeBiconnectedPlanar0.0070.0010.009
makeConnected0.0060.0010.007
makeMaximalPlanar0.0080.0010.009
maxClique0.0150.0020.016
maxFlow0.0120.0000.014
minCut0.0080.0010.009
mstree.kruskal0.0200.0020.023
mstree.prim0.0060.0010.007
ordering0.0090.0010.010
planarCanonicalOrdering0.0100.0010.011
planarFaceTraversal0.0060.0010.007
removeSelfLoops0.0080.0000.008
separates0.0080.0000.009
sp.between0.0180.0020.020
strongComp0.0080.0010.009
transClosure0.0100.0010.011
transitivity0.0060.0010.007
tsort0.0050.0030.006
wavefront0.0070.0010.008