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CHECK report for RBGL on malbec2

This page was generated on 2019-10-16 11:55:13 -0400 (Wed, 16 Oct 2019).

Package 1315/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.60.0
Bioconductor Package Maintainer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RBGL
Branch: RELEASE_3_9
Last Commit: ef24c17
Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.60.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RBGL.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RBGL_1.60.0.tar.gz
StartedAt: 2019-10-16 04:18:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:18:51 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 45.6 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RBGL.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RBGL_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RBGL.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.60.0’
* 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 27.5Mb
  sub-directories of 1Mb or more:
    libs       24.9Mb
    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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-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-3.9-bioc/meat/RBGL.Rcheck/00check.log’
for details.

Installation output

RBGL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RBGL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘RBGL’ ...
** using staged installation
checking R package BH ... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from bbc.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from cliques.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from clusteringCoef.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from dominatorTree.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from edmonds_optimum_branching.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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::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::value_type          weight_t;
                                                                       ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from hcs.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from mincut.hpp:4:0,
                 from hcs.cpp:2:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list; OutputIterator = std::back_insert_iterator >]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from incrConnComp.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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-3.9-bioc/R/library/BH/include/boost/foreach.hpp:1107:14: 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-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from interfaces.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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::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-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-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; OutputIterator = std::back_insert_iterator > >; Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long unsigned int>, long unsigned int, long unsigned int&>; Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long unsigned int>, long unsigned int, long unsigned int&>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)& ei +48)’ was declared here
       typename graph_traits::edge_iterator ei, eiend;
                                                   ^~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:33:0,
                 from RBGL.hpp:38,
                 from minST.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/edge.hpp:27:34: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ 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-3.9-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ was declared here
       typename graph_traits::edge_iterator ei, eiend;
                                                   ^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-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-3.9-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)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             INTEGER(eList)[i++] = source(*ei, flow_g);
             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223:0,
                 from RBGL.hpp:38,
                 from mincut.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:152:62: warning: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >::_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 > > > >*, std::vector > > > >, std::allocator > > > > > > >::_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-3.9-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator >]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from ordering.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/sparse_ordering.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/cuthill_mckee_ordering.hpp:15,
                 from ordering.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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::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::type id = get(vertex_index, g);
                                                ^~
ordering.cpp:176:53: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs]
   typedef graph_traits::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 Pair;
                                               ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from planar.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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-3.9-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::property >; PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator >*, std::vector > > >, boost::vec_adj_list_vertex_id_map, long unsigned int> >; ForwardIterator = __gnu_cxx::__normal_iterator >; GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long unsigned int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long unsigned int>]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12:0,
                 from planar.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function ‘void boost::boyer_myrvold_impl::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator > >; EdgeIndexMap = boost::adj_list_edge_property_map, boost::edge_index_t>; Graph = boost::adjacency_list, boost::property >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long unsigned int>; StoreOldHandlesPolicy = boost::graph::detail::store_old_handles; StoreEmbeddingPolicy = boost::graph::detail::no_embedding]’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1405:7: warning: ‘bicomp_root’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (bicomp_root != v)
       ^~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12,
                 from planar.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp: In static member function ‘static bool boost::maximum_cardinality_matching_verifier::verify_matching(const Graph&, MateMap, VertexIndexMap) [with Graph = R_adjacency_list; MateMap = long unsigned int*; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long unsigned int>]’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:124:64: 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-3.9-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:820:48: note: ‘*((void*)& occ +16)’ was declared here
       detail::odd_components_counter occ(num_odd_components);
                                                ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from registerSigHandlers.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-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::property >, boost::no_property, boost::listS>; Size = long unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: warning: ‘*((void*)(& i)+32).__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-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 >; Size = int; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; PredecessorMap = long unsigned int*; DistanceMap = double*; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:129:65: warning: ‘*((void*)(& i)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ 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-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from shortestPath.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: note: ‘*((void*)(& i)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ was declared here
     typename GTraits::edge_iterator i, end;
                                     ^
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: warning: ‘*((void*)(& i)+32).__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-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; DistanceMatrix = Basic2DMatrix; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; Zero = double]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:111:66: note: ‘*((void*)& first +48)’ was declared here
     typename graph_traits::edge_iterator first, last;
                                                                  ^~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:125:12: warning: ‘*((void*)(& first)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ 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-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-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; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, long unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]’:
/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/BH/include/boost/shared_array.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20,
                 from shortestPath.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         return px[i];
                ~~^
In file included from shortestPath.cpp:4:0:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: warning: ‘*((void*)(& e)+32).__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from shortestPath.cpp:1:
/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:87:37: warning: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ 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-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:39: warning: ‘*((void*)(& e)+32).__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >::_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-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 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-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-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::property >, boost::no_property, boost::listS>; Size = long unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]’:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28:0,
                 from sna.cpp:3:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:106:37: warning: ‘*((void*)(& i)+32).__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from RBGL.hpp:38,
                 from sna.cpp:1:
/home/biocbuild/bbs-3.9-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; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, long unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]’:
/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/BH/include/boost/property_map/shared_array_property_map.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:27,
                 from sna.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         return px[i];
                ~~^
In file included from sna.cpp:3:0:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: note: ‘*((void*)(& e)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ was declared here
     typename Traits2::edge_iterator e, e_end;
                                     ^
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:98:37: warning: ‘*((void*)(& e)+32).__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/bind.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind.hpp:22,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:223,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21,
                 from transitive_closure.cpp:16:
/home/biocbuild/bbs-3.9-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-3.9-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)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, long unsigned int, boost::detail::edge_desc_impl, long int>::m_src’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             INTEGER(eList)[i++] = source(*ei, TC);
             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.9-bioc/R/library/BH/include  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from RBGL.hpp:17,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from RBGL.hpp:38,
                 from wavefront.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-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 class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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

> BiocGenerics:::testPackage("RBGL")

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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



RUNIT TEST PROTOCOL -- Wed Oct 16 04:18:44 2019 
*********************************************** 
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 
  0.778   0.027   0.828

Example timings

RBGL.Rcheck/RBGL-Ex.timings

nameusersystemelapsed
FileDep0.4760.0080.497
astarSearch0.0720.0000.085
bandwidth0.0140.0000.015
bellman.ford.sp0.0500.0000.049
bfs0.0190.0000.049
biConnComp0.0060.0000.006
boyerMyrvoldPlanarityTest0.0080.0000.022
chrobakPayneStraightLineDrawing0.0390.0040.044
clusteringCoef0.0090.0000.009
clusteringCoefAppr0.0070.0000.007
coloring0.0040.0000.005
connectedComp0.0130.0000.013
dag.sp0.0060.0000.006
dijkstra.sp0.0190.0000.032
dominatorTree0.0110.0000.035
edgeConn0.0060.0000.006
edmondsMaxCardinalityMatching0.010.000.01
edmondsOptimumBranching0.0060.0000.006
extractPath0.0030.0000.003
floyd.warshall.all.pairs.sp0.0070.0000.007
gprofile0.0050.0000.005
graphGenerator0.0010.0000.001
highlyConnSG0.0090.0000.008
incrConnComp0.0060.0000.006
is.triangulated0.0120.0000.013
isKuratowskiSubgraph0.0080.0000.007
isStraightLineDrawing0.0080.0000.008
isomorphism0.0060.0040.010
johnson.all.pairs.sp0.0070.0000.063
kCliques0.0060.0000.007
kCores0.0350.0030.038
lambdaSets0.0090.0000.052
layout0.0010.0000.000
makeBiconnectedPlanar0.0090.0000.009
makeConnected0.0070.0000.007
makeMaximalPlanar0.0080.0000.008
maxClique0.0120.0000.012
maxFlow0.010.000.01
minCut0.0060.0000.006
mstree.kruskal0.0230.0000.071
mstree.prim0.0090.0000.009
ordering0.010.000.01
planarCanonicalOrdering0.0030.0030.006
planarFaceTraversal0.0070.0000.006
removeSelfLoops0.0090.0000.009
separates0.0140.0000.014
sp.between0.0220.0000.022
strongComp0.0110.0000.010
transClosure0.0080.0000.008
transitivity0.0060.0000.005
tsort0.0030.0000.004
wavefront0.0070.0000.008