Back to Multiple platform build/check report for BioC 3.14
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

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

CHECK 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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DNABarcodes.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DNABarcodes_1.24.0.tar.gz
StartedAt: 2022-04-12 18:48:20 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:49:59 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 99.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DNABarcodes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DNABarcodes.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DNABarcodes_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DNABarcodes.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DNABarcodes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DNABarcodes' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DNABarcodes' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analyse.barcodes : <anonymous>: no visible global function definition
  for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/DNABarcodes/libs/i386/DNABarcodes.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/DNABarcodes/libs/x64/DNABarcodes.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
create.dnabarcodes 9.36   0.01    4.88
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
create.dnabarcodes 5.92   0.04    3.05
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/DNABarcodes.Rcheck/00check.log'
for details.

Installation output

DNABarcodes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/DNABarcodes_1.24.0.tar.gz && 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 && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DNABarcodes_1.24.0.zip && rm DNABarcodes_1.24.0.tar.gz DNABarcodes_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 75  129k   75 99689    0     0   510k      0 --:--:-- --:--:-- --:--:--  509k
100  129k  100  129k    0     0   672k      0 --:--:-- --:--:-- --:--:--  672k

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)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DNABarcodes' successfully unpacked and MD5 sums checked

Tests output

Example timings

DNABarcodes.Rcheck/examples_i386/DNABarcodes-Ex.timings

nameusersystemelapsed
DNABarcodes-package2.070.021.08
analyse.barcodes0.010.000.02
barcode.set.distances0.010.000.02
create.dnabarcodes9.360.014.88
create.pool000
demultiplex2.200.062.26
distance000

DNABarcodes.Rcheck/examples_x64/DNABarcodes-Ex.timings

nameusersystemelapsed
DNABarcodes-package1.560.000.99
analyse.barcodes0.020.000.01
barcode.set.distances0.030.000.03
create.dnabarcodes5.920.043.05
create.pool000
demultiplex3.740.033.77
distance000