Multiple platform build/check report for BioC 3.20 - BUILD BIN results for DNABarcodes on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4503
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
BUILD BIN results for DNABarcodes on palomino8

To the developers/maintainers of the DNABarcodes package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: DNABarcodes
Version: 1.36.0
Command: rm -rf DNABarcodes.buildbin-libdir && mkdir DNABarcodes.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=DNABarcodes.buildbin-libdir DNABarcodes_1.36.0.tar.gz
StartedAt: 2024-11-01 07:39:10 -0400 (Fri, 01 Nov 2024)
EndedAt: 2024-11-01 07:40:47 -0400 (Fri, 01 Nov 2024)
EllapsedTime: 96.2 seconds
RetCode: 0
Status: OK
PackageFile: DNABarcodes_1.36.0.zip
PackageFileSize: 886.9 KiB
Command output

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###
### Running command:
###
###   rm -rf DNABarcodes.buildbin-libdir && mkdir DNABarcodes.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=DNABarcodes.buildbin-libdir DNABarcodes_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'DNABarcodes' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++17
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c DNABarcodes_init.c -o DNABarcodes_init.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c analyse_barcodes.cpp -o analyse_barcodes.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c barcode_set_distances.cpp -o barcode_set_distances.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cachedistance.cpp -o cachedistance.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/serialization/array.hpp:26,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from cachedistance.cpp:8:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/traits.hpp:21,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:27:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  111 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_algobase.h:65,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/specfun.h:43,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/cmath:3699,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cachedistance.cpp:4:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  149 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chromosome.cpp -o chromosome.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-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:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from chromosome.cpp:15:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c code_falsification.cpp -o code_falsification.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-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:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from code_falsification.cpp:26:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c conway.cpp -o conway.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-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:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from conway.cpp:11:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_distance_func.cpp -o create_distance_func.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/serialization/array.hpp:26,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from create_distance_func.cpp:9:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/traits.hpp:21,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:27:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  111 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_algobase.h:65,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/specfun.h:43,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/cmath:3699,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_distance_func.cpp:3:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  149 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from create_dnabarcodes.cpp:13:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/pointer_cast.hpp:52,
                 from create_dnabarcodes.cpp:14:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/traits.hpp:21,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:27,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from create_dnabarcodes.cpp:21:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  111 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_algobase.h:65,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/specfun.h:43,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/cmath:3699,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from create_dnabarcodes.cpp:3:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  149 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from F:/biocbuild/bbs-3.20-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:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   75 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_pool.cpp -o create_pool.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from create_pool.cpp:6:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c demultiplex.cpp -o demultiplex.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c distance_for_R.cpp -o distance_for_R.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c genericchromosome.cpp -o genericchromosome.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c greedyevolution.cpp -o greedyevolution.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from greedyevolution.cpp:12:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hammingdistance.cpp -o hammingdistance.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c helpers.cpp -o helpers.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c levenshteindistance.cpp -o levenshteindistance.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from F:/biocbuild/bbs-3.20-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:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   75 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/unordered/detail/opt_storage.hpp:11,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/unordered/detail/archive_constructed.hpp:12,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/unordered/detail/serialize_container.hpp:14,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/unordered/detail/serialize_fca_container.hpp:12,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:17,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phaseshiftdist.cpp -o phaseshiftdist.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from phaseshiftdist.cpp:23:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequence.cpp -o sequence.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from sequence.cpp:3:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequence.cpp:10:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequencepool.cpp -o sequencepool.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78,
                 from sequencepool.cpp:9:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.20-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>&&)':
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from sequencepool.cpp:16:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++ -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/meat/DNABarcodes.buildbin-libdir/00LOCK-DNABarcodes/00new/DNABarcodes/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* MD5 sums
packaged installation of 'DNABarcodes' as DNABarcodes_1.36.0.zip
* DONE (DNABarcodes)