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This page was generated on 2021-07-23 15:05:48 -0400 (Fri, 23 Jul 2021).

INSTALL results for RBGL on nebbiolo1

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: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RBGL
StartedAt: 2021-07-22 06:05:07 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 06:06:51 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 104.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RBGL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘RBGL’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bbc.cpp -o bbc.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cliques.cpp -o cliques.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c clusteringCoef.cpp -o clusteringCoef.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
clusteringCoef.cpp: In function ‘SEXPREC* graphGenerator(SEXP, SEXP, SEXP)’:
clusteringCoef.cpp:394:40: warning: ‘u’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  394 |         Graph_ud::vertex_descriptor v, u, w=Graph_ud::null_vertex();
      |                                        ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dominatorTree.cpp -o dominatorTree.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from edmonds_optimum_branching.hpp:94,
                 from edmonds_optimum_branching.cpp:3:
edmonds_optimum_branching_impl.hpp: In function ‘void edmonds_optimum_branching(TEdgeListGraph&, TVertexIndexMap, TWeightMap, TInputIterator, TInputIterator, TOutputIterator)’:
edmonds_optimum_branching_impl.hpp:520:71: warning: typedef ‘EdgeIter’ locally defined but not used [-Wunused-local-typedefs]
  520 |     typedef typename graph_traits<TEdgeListGraph>::edge_iterator      EdgeIter;
      |                                                                       ^~~~~~~~
edmonds_optimum_branching_impl.hpp:521:71: warning: typedef ‘weight_t’ locally defined but not used [-Wunused-local-typedefs]
  521 |     typedef typename property_traits<TWeightMap>::value_type          weight_t;
      |                                                                       ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c hcs.cpp -o hcs.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from mincut.hpp:4,
                 from hcs.cpp:2:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   33 |         typename Traits::vertex_descriptor p;
      |                                            ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c incrConnComp.cpp -o incrConnComp.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from incrConnComp.cpp:2:
incrConnComp.cpp: In function ‘SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)’:
incrConnComp.cpp:74:32: warning: unused variable ‘child_index’ [-Wunused-variable]
   74 |      BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
      |                                ^~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:1114:14: note: in definition of macro ‘BOOST_FOREACH’
 1114 |         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
      |              ^~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c interfaces.cpp -o interfaces.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
interfaces.cpp: In function ‘SEXPREC* BGL_tsort_D(SEXP, SEXP, SEXP)’:
interfaces.cpp:81:17: warning: catching polymorphic type ‘struct boost::not_a_dag’ by value [-Wcatch-value=]
   81 |         catch ( not_a_dag )
      |                 ^~~~~~~~~
interfaces.cpp:57:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
   57 |         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
      |                                                            ^~~~
interfaces.cpp:61:62: warning: typedef ‘Color’ locally defined but not used [-Wunused-local-typedefs]
   61 |         typedef property_map<Graph_dd, vertex_color_t>::type Color;
      |                                                              ^~~~~
interfaces.cpp: In function ‘SEXPREC* BGL_bfs_D(SEXP, SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:98:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
   98 |         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
      |                                                            ^~~~
interfaces.cpp:99:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
   99 |         typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
interfaces.cpp: In function ‘SEXPREC* BGL_dfs_D(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:142:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
  142 |         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
      |                                                            ^~~~
interfaces.cpp:143:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
  143 |         typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
interfaces.cpp: In function ‘SEXPREC* BGL_connected_components_U(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:198:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
  198 |         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
      |                                                            ^~~~
interfaces.cpp:199:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
  199 |         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
interfaces.cpp: In function ‘SEXPREC* BGL_strong_components_D(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:225:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
  225 |         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
      |                                                            ^~~~
interfaces.cpp:226:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
  226 |         typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
interfaces.cpp: In function ‘SEXPREC* BGL_biconnected_components_U(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:252:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
  252 |         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
      |                                                            ^~~~
interfaces.cpp:253:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
  253 |         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
interfaces.cpp: In function ‘SEXPREC* BGL_articulation_points_U(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:295:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
  295 |         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
      |                                                            ^~~~
interfaces.cpp: In function ‘SEXPREC* BGL_edge_connectivity_U(SEXP, SEXP, SEXP, SEXP)’:
interfaces.cpp:320:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
  320 |         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
interfaces.cpp: In function ‘SEXPREC* BGL_sequential_vertex_coloring(SEXP, SEXP, SEXP)’:
interfaces.cpp:360:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
  360 |         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
      |                                                            ^~~~
interfaces.cpp:361:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
  361 |         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
In file included from interfaces.cpp:7:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   33 |         typename Traits::vertex_descriptor p;
      |                                            ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c minST.cpp -o minST.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
minST.cpp: In function ‘SEXPREC* BGL_KMST_D(SEXP, SEXP, SEXP, SEXP)’:
minST.cpp:14:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
   14 |         typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
minST.cpp: In function ‘SEXPREC* BGL_KMST_U(SEXP, SEXP, SEXP, SEXP)’:
minST.cpp:48:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
   48 |         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
      |                                                              ^~~~~~
minST.cpp: In function ‘SEXPREC* BGL_PRIM_U(SEXP, SEXP, SEXP, SEXP)’:
minST.cpp:81:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
   81 |         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
      |                                                            ^~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list<boost::directedS, double>; OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > >; Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, long unsigned int, long unsigned int&>; Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, long unsigned int, long unsigned int&>; Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
In file included from minST.cpp:2:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: ‘*((void*)& ei +48)’ was declared here
   78 |         typename graph_traits< Graph >::edge_iterator ei, eiend;
      |                                                       ^~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:32,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/edge.hpp:27:71: warning: ‘*((void*)& ei +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   27 |         inline edge_base(Vertex s, Vertex d) : m_source(s), m_target(d) {}
      |                                                                       ^
In file included from minST.cpp:2:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: ‘*((void*)& ei +40)’ was declared here
   78 |         typename graph_traits< Graph >::edge_iterator ei, eiend;
      |                                                       ^~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mincut.cpp -o mincut.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_max_flow_internal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, E_MF_METHOD)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
mincut.cpp:99:19: note: ‘*((void*)& ei +48)’ was declared here
   99 |     edge_iterator ei, e_end;
      |                   ^~
mincut.cpp:103:33: warning: ‘*((void*)& ei +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  103 |             INTEGER(eList)[i++] = source(*ei, flow_g);
      |             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:147:48: warning: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, 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, long unsigned int> > > > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, 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, long unsigned int> > > > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, 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, long unsigned int> > > > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  147 |                 &(*this->base()).get_property());
      |                                                ^
mincut.cpp:99:19: note: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, 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, long unsigned int> > > > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, 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, long unsigned int> > > > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, 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, long unsigned int> > > > > > > >::_M_current’ was declared here
   99 |     edge_iterator ei, e_end;
      |                   ^~
In file included from mincut.hpp:4,
                 from mincut.cpp:2:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   33 |         typename Traits::vertex_descriptor p;
      |                                            ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ordering.cpp -o ordering.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/sparse_ordering.hpp:24,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/cuthill_mckee_ordering.hpp:15,
                 from ordering.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma 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.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
ordering.cpp: In function ‘SEXPREC* BGL_min_degree_ordering(SEXP, SEXP, SEXP, SEXP)’:
ordering.cpp:133:53: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
  133 |   typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
      |                                                     ^~~~~~
ordering.cpp: In function ‘SEXPREC* BGL_king_ordering(SEXP, SEXP, SEXP, SEXP)’:
ordering.cpp:182:48: warning: variable ‘id’ set but not used [-Wunused-but-set-variable]
  182 |   property_map<Graph_dd, vertex_index_t>::type id = get(vertex_index, g);
      |                                                ^~
ordering.cpp:176:53: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
  176 |   typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
      |                                                     ^~~~~~
ordering.cpp: In function ‘SEXPREC* BGL_sloan_ordering(SEXP, SEXP, SEXP, SEXP, SEXP)’:
ordering.cpp:232:47: warning: typedef ‘Pair’ locally defined but not used [-Wunused-local-typedefs]
  232 |   typedef std::pair<std::size_t, std::size_t> Pair;
      |                                               ^~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c planar.cpp -o planar.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
planar.cpp: In function ‘SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)’:
planar.cpp:161:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int>, std::allocator<std::vector<long unsigned int> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  161 |            for ( int i = 0; i < v_vis.f_vis.size(); i++ )
      |                             ~~^~~~~~~~~~~~~~~~~~~~
planar.cpp:165:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  165 |                 for ( int j = 0; j < v_vis.f_vis[i].size(); j++ )
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~
planar.cpp: In function ‘SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)’:
planar.cpp:256:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  256 |     for ( int i = 0; i < ordering.size(); i++ )
      |                      ~~^~~~~~~~~~~~~~~~~
planar.cpp:225:34: warning: variable ‘oi_end’ set but not used [-Wunused-but-set-variable]
  225 |       Vertex_Vec_t::iterator oi, oi_end = ordering.end();
      |                                  ^~~~~~
planar.cpp: In function ‘SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)’:
planar.cpp:369:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >, boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int>, boost::no_property, boost::listS>::config::vertices_size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  369 |  for ( int i = 0, j = 0; i < num_vertices(g); i++ )
      |                          ~~^~~~~~~~~~~~~~~~~
planar.cpp: In function ‘SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)’:
planar.cpp:429:36: warning: variable ‘ki_end’ set but not used [-Wunused-but-set-variable]
  429 |           Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.end();
      |                                    ^~~~~~
planar.cpp:461:6: warning: unused variable ‘i’ [-Wunused-variable]
  461 |  int i, j = 0;
      |      ^
In file included from planar.cpp:6:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp: In function ‘void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, VertexIndexMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >; PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int> >; ForwardIterator = __gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >; GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<coord_t*, std::vector<coord_t> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp:207:22: warning: ‘next_to_rightmost’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  207 |             vertex_t next_to_rightmost;
      |                      ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12,
                 from planar.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function ‘void boost::boyer_myrvold_impl<Graph, VertexIndexMap, StoreOldHandlesPolicy, StoreEmbeddingPolicy>::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >; EdgeIndexMap = boost::adj_list_edge_property_map<boost::undirected_tag, int, const int&, long unsigned int, const boost::property<boost::edge_index_t, int>, boost::edge_index_t>; Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>; StoreOldHandlesPolicy = boost::graph::detail::store_old_handles; StoreEmbeddingPolicy = boost::graph::detail::no_embedding]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1616:22: warning: ‘bicomp_root’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1616 |         while (child != parent)
      |                ~~~~~~^~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12,
                 from planar.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/named_function_params.hpp: In static member function ‘static bool boost::maximum_cardinality_matching_verifier<Graph, MateMap, VertexIndexMap>::verify_matching(const Graph&, MateMap, VertexIndexMap) [with Graph = R_adjacency_list<boost::undirectedS, int>; MateMap = long unsigned int*; VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:192:64: warning: ‘*((void*)& occ +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  192 |     bgl_named_params(T v, const Base& b) : m_value(v), m_base(b) {}
      |                                                                ^
In file included from planar.cpp:11:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:778:52: note: ‘*((void*)& occ +16)’ was declared here
  778 |         detail::odd_components_counter< v_size_t > occ(num_odd_components);
      |                                                    ^~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c registerSigHandlers.cpp -o registerSigHandlers.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c shortestPath.cpp -o shortestPath.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
shortestPath.cpp: In function ‘SEXPREC* BGL_dijkstra_shortest_paths_D(SEXP, SEXP, SEXP, SEXP, SEXP)’:
shortestPath.cpp:17:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
   17 |         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
      |                                                            ^~~~
shortestPath.cpp: In function ‘SEXPREC* BGL_dag_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)’:
shortestPath.cpp:136:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
  136 |         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
      |                                                            ^~~~
shortestPath.cpp: In function ‘SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXP, SEXP, SEXP, SEXP)’:
shortestPath.cpp:177:81: warning: typedef ‘Graph’ locally defined but not used [-Wunused-local-typedefs]
  177 |         property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
      |                                                                                 ^~~~~
shortestPath.cpp:180:39: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
  180 |         typedef std::pair < int, int >Edge;
      |                                       ^~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>; Size = long unsigned int; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>, boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here
  104 |     typename GTraits::edge_iterator i, end;
      |                                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::no_property, boost::property<boost::edge_weight_t, double, boost::no_property> >; Size = int; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>; PredecessorMap = long unsigned int*; DistanceMap = double*; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here
  104 |     typename GTraits::edge_iterator i, end;
      |                                     ^
In file included from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:129:65: warning: ‘*((void*)& i +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  129 |   inline const T& get(const T* pa, std::ptrdiff_t k) { return pa[k]; }
      |                                                               ~~^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +40)’ was declared here
  104 |     typename GTraits::edge_iterator i, end;
      |                                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: warning: ‘*((void*)(& i)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::floyd_warshall_all_pairs_shortest_paths(const VertexAndEdgeListGraph&, DistanceMatrix&, const WeightMap&, const BinaryPredicate&, const BinaryFunction&, const Infinity&, const Zero&) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>; DistanceMatrix = Basic2DMatrix<double>; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>; BinaryPredicate = std::less<double>; BinaryFunction = boost::closed_plus<double>; Infinity = double; Zero = double]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& first +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
In file included from shortestPath.cpp:7:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:101:68: note: ‘*((void*)& first +48)’ was declared here
  101 |     typename graph_traits< VertexAndEdgeListGraph >::edge_iterator first, last;
      |                                                                    ^~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:113:14: warning: ‘*((void*)& first +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  113 |         if (d[source(*first, g)][target(*first, g)] != inf)
      |             ~^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_bellman_ford_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
shortestPath.cpp:101:50: note: ‘*((void*)& ei +48)’ was declared here
  101 |         graph_traits< EdgeGraph >::edge_iterator ei, ei_end;
      |                                                  ^~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>; DistanceMatrix = Basic2DMatrix<double>; VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>; Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>; BinaryPredicate = std::less<double>; BinaryFunction = boost::closed_plus<double>; Infinity = double; DistanceZero = double]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
In file included from shortestPath.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +48)’ was declared here
  101 |     typename Traits2::edge_iterator e, e_end;
      |                                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_array.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20,
                 from shortestPath.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: ‘*((void*)& e +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  201 |         return px[i];
      |                ~~^
In file included from shortestPath.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +40)’ was declared here
  101 |     typename Traits2::edge_iterator e, e_end;
      |                                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: warning: ‘*((void*)(& e)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
In file included from shortestPath.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:41: note: ‘*((void*)& e +48)’ was declared here
   84 |         typename Traits1::edge_iterator e, e_end;
      |                                         ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:89:41: warning: ‘*((void*)& e +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   89 |             boost::tie(e2, z) = add_edge(
      |                                 ~~~~~~~~^
   90 |                 get(id1, source(*e, g1)) + 1, get(id1, target(*e, g1)) + 1, g2);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:41: warning: ‘*((void*)(& e)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   84 |         typename Traits1::edge_iterator e, e_end;
      |                                         ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sna.cpp -o sna.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
sna.cpp: In function ‘SEXPREC* lambdaSets(SEXP, SEXP, SEXP, SEXP)’:
sna.cpp:161:9: warning: variable ‘res_cap’ set but not used [-Wunused-but-set-variable]
  161 |         res_cap = get(edge_residual_capacity, flow_g);
      |         ^~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>; Size = long unsigned int; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28,
                 from sna.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here
  104 |     typename GTraits::edge_iterator i, end;
      |                                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>; DistanceMatrix = Basic2DMatrix<double>; VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>; Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>; BinaryPredicate = std::less<double>; BinaryFunction = boost::closed_plus<double>; Infinity = double; DistanceZero = double]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
In file included from sna.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +48)’ was declared here
  101 |     typename Traits2::edge_iterator e, e_end;
      |                                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/shared_array_property_map.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from sna.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: ‘*((void*)& e +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  201 |         return px[i];
      |                ~~^
In file included from sna.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +40)’ was declared here
  101 |     typename Traits2::edge_iterator e, e_end;
      |                                     ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c transitive_closure.cpp -o transitive_closure.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:30,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma 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.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:30,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_transitive_closure_D(SEXP, SEXP, SEXP)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |             if (edges BOOST_GRAPH_MEMBER first
      |             ^~
transitive_closure.cpp:43:33: note: ‘*((void*)& ei +48)’ was declared here
   43 |         Graph_dd::edge_iterator ei, e_end;
      |                                 ^~
transitive_closure.cpp:46:33: warning: ‘*((void*)& ei +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   46 |             INTEGER(eList)[i++] = source(*ei, TC);
      |             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c wavefront.cpp -o wavefront.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  465 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  478 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  561 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  570 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  572 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/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 -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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)