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CHECK report for RBGL on malbec2

This page was generated on 2020-10-17 11:55:31 -0400 (Sat, 17 Oct 2020).

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 1421/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.64.0
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RBGL
Branch: RELEASE_3_11
Last Commit: 2f5aeaf
Last Changed Date: 2020-04-27 14:08:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.64.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RBGL.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RBGL_1.64.0.tar.gz
StartedAt: 2020-10-17 04:31:35 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:32:15 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 40.0 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RBGL.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RBGL_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RBGL.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.64.0’
* 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 27.7Mb
  sub-directories of 1Mb or more:
    libs       25.1Mb
    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-3.11-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-3.11-bioc/meat/RBGL.Rcheck/00check.log’
for details.

Installation output

RBGL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RBGL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘RBGL’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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 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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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 mincut.hpp:4:0,
                 from hcs.cpp:2:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       typename Traits::vertex_descriptor p;
                                          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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 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-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
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-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       typename Traits::vertex_descriptor p;
                                          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
In file included from minST.cpp:2:0:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)& ei +48)’ was declared here
       typename graph_traits<Graph>::edge_iterator ei, eiend;
                                                   ^~
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:33:0,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/detail/edge.hpp:27:34: warning: ‘*((void*)& ei +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         : m_source(s), m_target(d) { }
                                  ^
In file included from minST.cpp:2:0:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)& ei +40)’ was declared here
       typename graph_traits<Graph>::edge_iterator ei, eiend;
                                                   ^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
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-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223:0,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:152:62: 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-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:32:42: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       typename Traits::vertex_descriptor p;
                                          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/detail/sparse_ordering.hpp:24,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/cuthill_mckee_ordering.hpp:15,
                 from ordering.cpp:3:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
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-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp:217:22: 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-3.11-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12:0,
                 from planar.cpp:3:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1406:7: warning: ‘bicomp_root’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (bicomp_root != v)
       ^~
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12,
                 from planar.cpp:3:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:127:64: 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-3.11-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:820:48: 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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)& i +48)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: 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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: 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-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)& i +40)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: 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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& first +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
In file included from shortestPath.cpp:7:0:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:111:66: note: ‘*((void*)& first +48)’ was declared here
     typename graph_traits<VertexAndEdgeListGraph>::edge_iterator first, last;
                                                                  ^~~~~
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:125:12: 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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
In file included from shortestPath.cpp:4:0:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)& e +48)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_array.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:27,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20,
                 from shortestPath.cpp:3:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)& e +40)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: 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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
In file included from shortestPath.cpp:4:0:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:39: note: ‘*((void*)& e +48)’ was declared here
       typename Traits1::edge_iterator e, e_end;
                                       ^
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:87:37: 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-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:39: 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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from sna.cpp:3:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)& i +48)’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: 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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
In file included from sna.cpp:3:0:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)& e +48)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/shared_array_property_map.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from sna.cpp:3:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)& e +40)’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: 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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second)
         ^~
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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.11-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;
                            ^~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-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-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, which.max, which.min



RUNIT TEST PROTOCOL -- Sat Oct 17 04:32:10 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RBGL RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.672   0.062   0.718

Example timings

RBGL.Rcheck/RBGL-Ex.timings

nameusersystemelapsed
FileDep0.3440.0080.363
astarSearch0.0420.0000.041
bandwidth0.0100.0000.009
bellman.ford.sp0.0300.0000.029
bfs0.0090.0000.009
biConnComp0.0040.0000.004
boyerMyrvoldPlanarityTest0.0050.0000.015
chrobakPayneStraightLineDrawing0.0320.0000.032
clusteringCoef0.0050.0000.006
clusteringCoefAppr0.0050.0000.004
coloring0.0030.0000.003
connectedComp0.0090.0000.008
dag.sp0.0050.0000.005
dijkstra.sp0.0040.0080.012
dominatorTree0.0040.0000.004
edgeConn0.0040.0000.003
edmondsMaxCardinalityMatching0.0060.0000.006
edmondsOptimumBranching0.0070.0000.007
extractPath0.0020.0000.002
floyd.warshall.all.pairs.sp0.0040.0010.005
gprofile0.0010.0020.003
graphGenerator000
highlyConnSG0.0060.0000.006
incrConnComp0.0050.0000.004
is.triangulated0.0080.0000.008
isKuratowskiSubgraph0.0050.0000.008
isStraightLineDrawing0.0050.0000.005
isomorphism0.0060.0000.006
johnson.all.pairs.sp0.0040.0000.005
kCliques0.0040.0000.005
kCores0.0240.0000.025
lambdaSets0.0050.0000.006
layout000
makeBiconnectedPlanar0.0060.0000.007
makeConnected0.0050.0000.004
makeMaximalPlanar0.0060.0000.005
maxClique0.0080.0000.007
maxFlow0.0070.0000.007
minCut0.0040.0000.003
mstree.kruskal0.0090.0040.013
mstree.prim0.0050.0000.004
ordering0.0060.0000.006
planarCanonicalOrdering0.0040.0000.004
planarFaceTraversal0.0070.0000.007
removeSelfLoops0.0060.0000.006
separates0.0070.0000.007
sp.between0.0150.0000.014
strongComp0.0070.0000.007
transClosure0.0050.0000.005
transitivity0.0030.0000.004
tsort0.0020.0000.002
wavefront0.0040.0000.004