Multiple platform build/check report for BioC 3.21 - CHECK results for DNABarcodes on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4566
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for DNABarcodes on palomino7

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: 1.38.0

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DNABarcodes.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings DNABarcodes_1.38.0.tar.gz

StartedAt: 2025-08-15 01:38:35 -0400 (Fri, 15 Aug 2025)

EndedAt: 2025-08-15 01:39:54 -0400 (Fri, 15 Aug 2025)

EllapsedTime: 78.9 seconds

RetCode: 0

Status: OK

CheckDir: DNABarcodes.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DNABarcodes.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings DNABarcodes_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/DNABarcodes.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DNABarcodes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DNABarcodes' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DNABarcodes' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking C++ specification ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    First development version for introduction to Bioconductor
  Cannot process chunk/lines:
    This is the first public release.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/DNABarcodes/libs/x64/DNABarcodes.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
create.dnabarcodes 5.31   0.04    2.85
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/DNABarcodes.Rcheck/00check.log'
for details.

Installation output

DNABarcodes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL DNABarcodes
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'DNABarcodes' ...
** this is package 'DNABarcodes' version '1.38.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++17
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c DNABarcodes_init.c -o DNABarcodes_init.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from analyse_barcodes.cpp:10:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from barcode_set_distances.cpp:10:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c cachedistance.cpp -o cachedistance.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from cachedistance.cpp:7:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array.hpp:26,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from cachedistance.cpp:8:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c chromosome.cpp -o chromosome.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-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:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from chromosome.cpp:15:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-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:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from code_falsification.cpp:26:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c conway.cpp -o conway.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-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:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from conway.cpp:11:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from create_distance_func.cpp:5:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array.hpp:26,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
                 from cachedistance.h:16,
                 from create_distance_func.cpp:9:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from create_dnabarcodes.cpp:13:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_dnabarcodes.cpp:17:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/pointer_cast.hpp:13,
                 from create_dnabarcodes.cpp:14:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from E:/biocbuild/bbs-3.21-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:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 ) noexcept : px( p.release() )
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from create_pool.cpp:6:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from create_pool.cpp:12:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c demultiplex.cpp -o demultiplex.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from demultiplex.cpp:9:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from distance_for_R.cpp:9:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from distance.h:11:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c greedyevolution.cpp -o greedyevolution.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from greedyevolution.h:8,
                 from greedyevolution.cpp:5:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from greedyevolution.cpp:12:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c hammingdistance.cpp -o hammingdistance.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from hammingdistance.cpp:7:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c levenshteindistance.cpp -o levenshteindistance.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from levenshteindistance.cpp:7:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from E:/biocbuild/bbs-3.21-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:
E:/biocbuild/bbs-3.21-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 ) noexcept : px( p.release() )
      |                               ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/unordered/detail/opt_storage.hpp:11,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/unordered/detail/archive_constructed.hpp:12,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/unordered/detail/serialize_container.hpp:14,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/unordered/detail/serialize_fca_container.hpp:12,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c phaseshiftdist.cpp -o phaseshiftdist.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from phaseshiftdist.cpp:10:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from phaseshiftdist.cpp:23:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c sequence.cpp -o sequence.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from sequence.cpp:3:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequence.cpp:13:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequence.cpp:10:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from sequencelevenshteindistance.cpp:3:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequence.h:13:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c sequencepool.cpp -o sequencepool.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from sequence.h:19,
                 from distance.h:14,
                 from sequencepool.cpp:11:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from sequencepool.cpp:9:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
E:/biocbuild/bbs-3.21-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>&&)':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76,
                 from sequencepool.cpp:16:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-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 |     );
      |     ~                
E:/biocbuild/bbs-3.21-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:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/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
* DONE (DNABarcodes)

Tests output

Example timings

DNABarcodes.Rcheck/DNABarcodes-Ex.timings

name	user	system	elapsed
DNABarcodes-package	1.06	0.00	0.55
analyse.barcodes	0.01	0.00	0.01
barcode.set.distances	0.01	0.00	0.01
create.dnabarcodes	5.31	0.04	2.85
create.pool	0	0	0
demultiplex	1.99	0.47	2.45
distance	0	0	0