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CHECK report for RBGL on malbec1

This page was generated on 2021-05-06 12:28:44 -0400 (Thu, 06 May 2021).

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

Summary

Package: RBGL
Version: 1.66.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RBGL.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RBGL_1.66.0.tar.gz
StartedAt: 2021-05-06 04:59:06 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:59:44 -0400 (Thu, 06 May 2021)
EllapsedTime: 38.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RBGL.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RBGL_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/RBGL.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.66.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RBGL’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs       25.0Mb
    old_boost   1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.12-bioc/R/library/RBGL/libs/RBGL.so’:
  Found ‘abort’, possibly from ‘abort’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/RBGL.Rcheck/00check.log’
for details.

Installation output

RBGL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL RBGL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘RBGL’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 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]
         Graph_ud::vertex_descriptor v, u, w=Graph_ud::null_vertex();
                                        ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-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++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from edmonds_optimum_branching.hpp:94:0,
                 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]
     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]
     typedef typename property_traits<TWeightMap>::value_type          weight_t;
                                                                       ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from mincut.hpp:4:0,
                 from hcs.cpp:2:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         typename Traits::vertex_descriptor p;
                                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from incrConnComp.cpp:2:0:
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]
      BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
                                ^
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/foreach.hpp:1114:14: note: in definition of macro ‘BOOST_FOREACH’
         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
              ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
interfaces.cpp: In function ‘SEXPREC* BGL_tsort_D(SEXP, SEXP, SEXP)’:
interfaces.cpp:57:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^~~~
interfaces.cpp:61:62: warning: typedef ‘Color’ locally defined but not used [-Wunused-local-typedefs]
         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]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^~~~
interfaces.cpp:99:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         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]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^~~~
interfaces.cpp:143:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         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]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^~~~
interfaces.cpp:199:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         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]
         typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                            ^~~~
interfaces.cpp:226:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         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]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^~~~
interfaces.cpp:253:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         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]
         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]
         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]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^~~~
interfaces.cpp:361:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
         typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                              ^~~~~~
In file included from interfaces.cpp:7:0:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         typename Traits::vertex_descriptor p;
                                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 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]
         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]
         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]
         typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                            ^~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
In file included from minST.cpp:2:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: ‘*((void*)& ei +48)’ was declared here
         typename graph_traits< Graph >::edge_iterator ei, eiend;
                                                       ^~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:32:0,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.12-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]
         inline edge_base(Vertex s, Vertex d) : m_source(s), m_target(d) {}
                                                                       ^
In file included from minST.cpp:2:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: ‘*((void*)& ei +40)’ was declared here
         typename graph_traits< Graph >::edge_iterator ei, eiend;
                                                       ^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
mincut.cpp:99:19: note: ‘*((void*)& ei +48)’ was declared here
     edge_iterator ei, e_end;
                   ^~
mincut.cpp:103:33: warning: ‘*((void*)& ei +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             INTEGER(eList)[i++] = source(*ei, flow_g);
             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255:0,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.12-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]
                 &(*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
     edge_iterator ei, e_end;
                   ^~
In file included from mincut.hpp:4:0,
                 from mincut.cpp:2:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         typename Traits::vertex_descriptor p;
                                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/sparse_ordering.hpp:24,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/cuthill_mckee_ordering.hpp:15,
                 from ordering.cpp:3:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/sparse_ordering.hpp:24:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/cuthill_mckee_ordering.hpp:15,
                 from ordering.cpp:3:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:41:1: 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.
 )
 ^
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]
   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]
   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]
   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]
   typedef std::pair<std::size_t, std::size_t> Pair;
                                               ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
planar.cpp: In function ‘SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)’:
planar.cpp:161:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
            for ( int i = 0; i < v_vis.f_vis.size(); i++ )
                             ~~^~~~~~~~~~~~~~~~~~~~
planar.cpp:165:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 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 between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < ordering.size(); i++ )
                      ~~^~~~~~~~~~~~~~~~~
planar.cpp:225:34: warning: variable ‘oi_end’ set but not used [-Wunused-but-set-variable]
       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 between signed and unsigned integer expressions [-Wsign-compare]
  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]
           Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.end();
                                    ^~~~~~
planar.cpp:461:6: warning: unused variable ‘i’ [-Wunused-variable]
  int i, j = 0;
      ^
In file included from planar.cpp:6:0:
/home/biocbuild/bbs-3.12-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-3.12-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]
             vertex_t next_to_rightmost;
                      ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12:0,
                 from planar.cpp:3:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1264:9: warning: ‘bicomp_root’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (bicomp_root != v)
         ^~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12,
                 from planar.cpp:3:
/home/biocbuild/bbs-3.12-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-3.12-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]
     bgl_named_params(T v, const Base& b) : m_value(v), m_base(b) {}
                                                                ^
In file included from planar.cpp:11:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:778:52: note: ‘*((void*)& occ +16)’ was declared here
         detail::odd_components_counter< v_size_t > occ(num_odd_components);
                                                    ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 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]
         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]
         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]
         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]
         typedef std::pair < int, int >Edge;
                                       ^~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
/home/biocbuild/bbs-3.12-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::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-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
In file included from RBGL.hpp:17:0,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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]
   inline const T& get(const T* pa, std::ptrdiff_t k) { return pa[k]; }
                                                               ~~^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +40)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
In file included from shortestPath.cpp:7:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:101:68: note: ‘*((void*)& first +48)’ was declared here
     typename graph_traits< VertexAndEdgeListGraph >::edge_iterator first, last;
                                                                    ^~~~~
/home/biocbuild/bbs-3.12-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]
         if (d[source(*first, g)][target(*first, g)] != inf)
             ~^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
shortestPath.cpp:101:50: note: ‘*((void*)& ei +48)’ was declared here
         graph_traits< EdgeGraph >::edge_iterator ei, ei_end;
                                                  ^~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
In file included from shortestPath.cpp:4:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +48)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/shared_array.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20,
                 from shortestPath.cpp:3:
/home/biocbuild/bbs-3.12-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]
         return px[i];
                ~~^
In file included from shortestPath.cpp:4:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +40)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
In file included from shortestPath.cpp:4:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:41: note: ‘*((void*)& e +48)’ was declared here
         typename Traits1::edge_iterator e, e_end;
                                         ^
/home/biocbuild/bbs-3.12-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]
             boost::tie(e2, z) = add_edge(
                                 ~~~~~~~~^
                 get(id1, source(*e, g1)) + 1, get(id1, target(*e, g1)) + 1, g2);
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.12-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]
         typename Traits1::edge_iterator e, e_end;
                                         ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 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]
         res_cap = get(edge_residual_capacity, flow_g);
         ^~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from sna.cpp:3:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
/home/biocbuild/bbs-3.12-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::property<boost::edge_weight2_t, double, boost::no_property> > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
In file included from sna.cpp:3:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +48)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/shared_array_property_map.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from sna.cpp:3:
/home/biocbuild/bbs-3.12-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]
         return px[i];
                ~~^
In file included from sna.cpp:3:0:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +40)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
/home/biocbuild/bbs-3.12-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, boost::no_property> > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16:0,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:41:1: 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.
 )
 ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/reverse_graph.hpp:9,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transpose_graph.hpp:16,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/strong_components.hpp:267,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.12-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-3.12-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]
             if (edges BOOST_GRAPH_MEMBER first
             ^~
transitive_closure.cpp:43:33: note: ‘*((void*)& ei +48)’ was declared here
         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]
             INTEGER(eList)[i++] = source(*ei, TC);
             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-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]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from RBGL.hpp:38,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from RBGL.hpp:38,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)

Tests output

RBGL.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("RBGL")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min



RUNIT TEST PROTOCOL -- Thu May  6 04:59:40 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RBGL RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.024   0.048   1.114

Example timings

RBGL.Rcheck/RBGL-Ex.timings

nameusersystemelapsed
FileDep0.6200.0040.645
astarSearch0.0720.0000.084
bandwidth0.0160.0000.017
bellman.ford.sp0.0520.0000.062
bfs0.0160.0000.015
biConnComp0.0080.0000.007
boyerMyrvoldPlanarityTest0.0080.0000.009
chrobakPayneStraightLineDrawing0.0560.0000.055
clusteringCoef0.0080.0000.009
clusteringCoefAppr0.0080.0000.008
coloring0.0040.0000.005
connectedComp0.0160.0000.030
dag.sp0.0120.0000.012
dijkstra.sp0.0240.0000.024
dominatorTree0.0080.0000.007
edgeConn0.0080.0000.007
edmondsMaxCardinalityMatching0.0120.0000.013
edmondsOptimumBranching0.0120.0000.014
extractPath0.0000.0000.004
floyd.warshall.all.pairs.sp0.0080.0000.009
gprofile0.0080.0000.013
graphGenerator0.0000.0000.001
highlyConnSG0.0120.0000.010
incrConnComp0.0080.0000.007
is.triangulated0.0120.0000.014
isKuratowskiSubgraph0.0080.0000.009
isStraightLineDrawing0.0080.0040.010
isomorphism0.0120.0000.012
johnson.all.pairs.sp0.0080.0000.019
kCliques0.0040.0000.016
kCores0.0440.0000.045
lambdaSets0.0120.0000.009
layout0.0000.0000.001
makeBiconnectedPlanar0.0120.0000.012
makeConnected0.0120.0000.009
makeMaximalPlanar0.0080.0000.010
maxClique0.0120.0000.014
maxFlow0.0120.0000.012
minCut0.0040.0000.007
mstree.kruskal0.0160.0040.024
mstree.prim0.0040.0000.007
ordering0.0080.0000.011
planarCanonicalOrdering0.0120.0000.014
planarFaceTraversal0.0080.0000.007
removeSelfLoops0.0120.0000.011
separates0.0160.0000.013
sp.between0.0280.0000.029
strongComp0.0160.0000.013
transClosure0.0120.0000.011
transitivity0.0080.0000.007
tsort0.0040.0000.005
wavefront0.0080.0000.007