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This page was generated on 2022-04-13 12:06:28 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for DNABarcodes on tokay2


To the developers/maintainers of the DNABarcodes package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DNABarcodes.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 531/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNABarcodes 1.24.0  (landing page)
Tilo Buschmann
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/DNABarcodes
git_branch: RELEASE_3_14
git_last_commit: 4fee550
git_last_commit_date: 2021-10-26 12:22:37 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DNABarcodes
Version: 1.24.0
Command: rm -rf DNABarcodes.buildbin-libdir && mkdir DNABarcodes.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DNABarcodes.buildbin-libdir DNABarcodes_1.24.0.tar.gz
StartedAt: 2022-04-13 06:05:15 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 06:09:20 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 245.7 seconds
RetCode: 0
Status:   OK  
PackageFile: DNABarcodes_1.24.0.zip
PackageFileSize: 1.323 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DNABarcodes.buildbin-libdir && mkdir DNABarcodes.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DNABarcodes.buildbin-libdir DNABarcodes_1.24.0.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'DNABarcodes' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DNABarcodes_init.c -o DNABarcodes_init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c analyse_barcodes.cpp -o analyse_barcodes.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c barcode_set_distances.cpp -o barcode_set_distances.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cachedistance.cpp -o cachedistance.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array.hpp:26,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from cachedistance.cpp:8:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chromosome.cpp -o chromosome.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from chromosome.cpp:15:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c code_falsification.cpp -o code_falsification.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from code_falsification.cpp:26:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c conway.cpp -o conway.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from conway.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_distance_func.cpp -o create_distance_func.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array.hpp:26,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from create_distance_func.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from create_dnabarcodes.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from create_dnabarcodes.cpp:26:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_pool.cpp -o create_pool.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from create_pool.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c demultiplex.cpp -o demultiplex.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c distance_for_R.cpp -o distance_for_R.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c genericchromosome.cpp -o genericchromosome.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c greedyevolution.cpp -o greedyevolution.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from greedyevolution.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hammingdistance.cpp -o hammingdistance.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c helpers.cpp -o helpers.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c levenshteindistance.cpp -o levenshteindistance.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phaseshiftdist.cpp -o phaseshiftdist.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from phaseshiftdist.cpp:23:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequence.cpp -o sequence.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from sequence.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequencepool.cpp -o sequencepool.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from sequencepool.cpp:16:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DNABarcodes.dll tmp.def DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/DNABarcodes.buildbin-libdir/00LOCK-DNABarcodes/00new/DNABarcodes/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DNABarcodes'
    finding HTML links ... done
    DNABarcodes-package                     html  
    analyse.barcodes                        html  
    barcode.set.distances                   html  
    create.dnabarcodes                      html  
    create.pool                             html  
    demultiplex                             html  
    distance                                html  
    mutatedReads                            html  
    supplierSet                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DNABarcodes' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DNABarcodes_init.c -o DNABarcodes_init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c analyse_barcodes.cpp -o analyse_barcodes.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from analyse_barcodes.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c barcode_set_distances.cpp -o barcode_set_distances.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from barcode_set_distances.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cachedistance.cpp -o cachedistance.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array.hpp:26,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from cachedistance.cpp:8:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chromosome.cpp -o chromosome.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from chromosome.h:6,
                 from chromosome.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from chromosome.cpp:15:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c code_falsification.cpp -o code_falsification.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from chromosome.h:6,
                 from code_falsification.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from code_falsification.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from code_falsification.cpp:26:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c conway.cpp -o conway.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from conway.h:8,
                 from conway.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance.h:8,
                 from conway.h:8,
                 from conway.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from conway.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_distance_func.cpp -o create_distance_func.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/serialization/array.hpp:26,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from create_distance_func.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from create_dnabarcodes.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from create_dnabarcodes.cpp:26:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_pool.cpp -o create_pool.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from create_pool.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_pool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c demultiplex.cpp -o demultiplex.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from demultiplex.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c distance_for_R.cpp -o distance_for_R.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from distance_for_R.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c genericchromosome.cpp -o genericchromosome.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c greedyevolution.cpp -o greedyevolution.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from greedyevolution.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from greedyevolution.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hammingdistance.cpp -o hammingdistance.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from hammingdistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c helpers.cpp -o helpers.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c levenshteindistance.cpp -o levenshteindistance.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from levenshteindistance.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from maxclique.h:12,
                 from maxclique_pattabiraman_heuristic.h:10,
                 from maxclique_pattabiraman_heuristic.cpp:6:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from maxclique_pattabiraman_heuristic.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phaseshiftdist.cpp -o phaseshiftdist.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from phaseshiftdist.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from phaseshiftdist.cpp:23:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequence.cpp -o sequence.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from sequence.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.cpp:10:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from sequence.h:13,
                 from sequencelevenshteindistance.cpp:3:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequencepool.cpp -o sequencepool.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from sequencepool.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from sequencepool.cpp:16:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DNABarcodes.dll tmp.def DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/DNABarcodes.buildbin-libdir/DNABarcodes/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DNABarcodes' as DNABarcodes_1.24.0.zip
* DONE (DNABarcodes)