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CHECK report for pqsfinder on tokay2

This page was generated on 2020-10-17 11:57:26 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE pqsfinder PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1340/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 2.4.0
Jiri Hon
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/pqsfinder
Branch: RELEASE_3_11
Last Commit: 1b8fd23
Last Changed Date: 2020-04-27 14:56:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pqsfinder
Version: 2.4.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pqsfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pqsfinder_2.4.0.tar.gz
StartedAt: 2020-10-17 07:01:36 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:07:24 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 348.1 seconds
RetCode: 0
Status:  OK  
CheckDir: pqsfinder.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pqsfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pqsfinder_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pqsfinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pqsfinder' version '2.4.0'
* package encoding: UTF-8
* 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 'pqsfinder' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    lib    3.8Mb
    libs   3.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'BH' is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/pqsfinder/libs/i386/pqsfinder.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/pqsfinder/libs/x64/pqsfinder.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.Rcheck/00check.log'
for details.

Installation output

pqsfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pqsfinder_2.4.0.tar.gz && rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pqsfinder.buildbin-libdir pqsfinder_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pqsfinder_2.4.0.zip && rm pqsfinder_2.4.0.tar.gz pqsfinder_2.4.0.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  108k  100  108k    0     0  1820k      0 --:--:-- --:--:-- --:--:-- 2041k

install for i386

* installing *source* package 'pqsfinder' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pqsfinder.cpp -o pqsfinder.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pqsfinder.cpp: In function 'void find_all_runs(SEXP, int, std::__cxx11::basic_string<char>::const_iterator, std::__cxx11::basic_string<char>::const_iterator, run_match*, const regex&, const opts_t&, const scoring&, const const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)':
pqsfinder.cpp:584:53: warning: 'loop_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
           pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
                                      ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/winstances.cpp -o boost_regex/winstances.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/instances.cpp -o boost_regex/instances.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex.cpp -o boost_regex/regex.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/icu.cpp -o boost_regex/icu.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/cregex.cpp -o boost_regex/cregex.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
mkdir -p "C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386"
"C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386/libboost_regex.a" boost_regex/regex_raw_buffer.o boost_regex/static_mutex.o boost_regex/winstances.o boost_regex/regex_debug.o boost_regex/wc_regex_traits.o boost_regex/c_regex_traits.o boost_regex/w32_regex_traits.o boost_regex/instances.o boost_regex/wide_posix_api.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/usinstances.o boost_regex/cregex.o boost_regex/cpp_regex_traits.o boost_regex/regex_traits_defaults.o
C:\rtools40\mingw32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386/libboost_regex.a
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o pqsfinder.dll tmp.def RcppExports.o pqsfinder.o C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386/libboost_regex.a -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pqsfinder'
    finding HTML links ... done
    PQSViews-class                          html  
    finding level-2 HTML links ... done

    PQSViews                                html  
    as.character-PQSViews-method            html  
    density-PQSViews-method                 html  
    maxScores-PQSViews-method               html  
    maxScores                               html  
    pqsfinder                               html  
    score-PQSViews-method                   html  
    show-PQSViews-method                    html  
    strand-PQSViews-method                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'pqsfinder' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c pqsfinder.cpp -o pqsfinder.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
pqsfinder.cpp: In function 'void find_all_runs(SEXP, int, std::__cxx11::basic_string<char>::const_iterator, std::__cxx11::basic_string<char>::const_iterator, run_match*, const regex&, const opts_t&, const scoring&, const const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)':
pqsfinder.cpp:584:53: warning: 'loop_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
           pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
                                      ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/winstances.cpp -o boost_regex/winstances.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from boost_regex/wc_regex_traits.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/instances.cpp -o boost_regex/instances.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex.cpp -o boost_regex/regex.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/icu.cpp -o boost_regex/icu.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/cregex.cpp -o boost_regex/cregex.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
mkdir -p "C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64"
"C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a" boost_regex/regex_raw_buffer.o boost_regex/static_mutex.o boost_regex/winstances.o boost_regex/regex_debug.o boost_regex/wc_regex_traits.o boost_regex/c_regex_traits.o boost_regex/w32_regex_traits.o boost_regex/instances.o boost_regex/wide_posix_api.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/usinstances.o boost_regex/cregex.o boost_regex/cpp_regex_traits.o boost_regex/regex_traits_defaults.o
C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o pqsfinder.dll tmp.def RcppExports.o pqsfinder.o C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pqsfinder' as pqsfinder_2.4.0.zip
* DONE (pqsfinder)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pqsfinder' successfully unpacked and MD5 sums checked

Tests output

pqsfinder.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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

> library(testthat)
> library(pqsfinder)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

> 
> test_check("pqsfinder")
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
 compare pqsfinder_1_4_4_d, pqsfinder_1_4_4_r
 run default pqsfinder
Searching on sense strand...
Search status: finished              
 run pqsfinder using boost regex engine
Searching on sense strand...
Search status: finished              
 compare pv_d, pv_r
 compare pv_d, pqsfinder_1_4_4_d
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 30% ETTC 00:00:00
Search status: 43% ETTC 00:00:01
Search status: 46% ETTC 00:00:01
Search status: 47% ETTC 00:00:02
Search status: 48% ETTC 00:00:03
Search status: 49% ETTC 00:00:03
Search status: 55% ETTC 00:00:03
Search status: 59% ETTC 00:00:02
Search status: 78% ETTC 00:00:01
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 23% ETTC 00:00:00
Search status: 42% ETTC 00:00:00
Search status: 46% ETTC 00:00:01
Search status: 51% ETTC 00:00:01
Search status: 57% ETTC 00:00:01
Search status: 83% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 42% ETTC 00:00:00
Search status: 86% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 45% ETTC 00:00:00
Search status: 93% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 42% ETTC 00:00:00
Search status: 86% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 45% ETTC 00:00:00
Search status: 93% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 46% ETTC 00:00:00
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 46% ETTC 00:00:00
Search status: 98% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 46% ETTC 00:00:00
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 46% ETTC 00:00:00
Search status: 98% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 3% ETTC 00:00:32
Search status: 5% ETTC 00:00:38
Search status: 6% ETTC 00:00:47
Search status: 8% ETTC 00:00:46
Search status: 8% ETTC 00:01:09
Search status: 9% ETTC 00:01:20
Search status: 12% ETTC 00:01:06
Search status: 13% ETTC 00:01:13
Search status: 14% ETTC 00:01:13
Search status: 16% ETTC 00:01:08
Search status: 21% ETTC 00:00:52
Search status: 25% ETTC 00:00:48
Search status: 29% ETTC 00:00:41
Search status: 32% ETTC 00:00:38
Search status: 35% ETTC 00:00:35
Search status: 38% ETTC 00:00:34
Search status: 40% ETTC 00:00:33
Search status: 42% ETTC 00:00:33
Search status: 43% ETTC 00:00:34
Search status: 43% ETTC 00:00:37
Search status: 44% ETTC 00:00:36
Search status: 45% ETTC 00:00:37
Search status: 45% ETTC 00:00:39
Search status: 49% ETTC 00:00:34
Search status: 52% ETTC 00:00:32
Search status: 55% ETTC 00:00:29
Search status: 58% ETTC 00:00:27
Search status: 58% ETTC 00:00:28
Search status: 61% ETTC 00:00:26
Search status: 61% ETTC 00:00:27
Search status: 62% ETTC 00:00:27
Search status: 65% ETTC 00:00:24
Search status: 67% ETTC 00:00:23
Search status: 68% ETTC 00:00:22
Search status: 69% ETTC 00:00:22
Search status: 71% ETTC 00:00:20
Search status: 72% ETTC 00:00:20
Search status: 76% ETTC 00:00:16
Search status: 79% ETTC 00:00:14
Search status: 83% ETTC 00:00:11
Search status: 86% ETTC 00:00:09
Search status: 87% ETTC 00:00:08
Search status: 88% ETTC 00:00:07
Search status: 92% ETTC 00:00:05
Search status: 93% ETTC 00:00:04
Search status: 95% ETTC 00:00:03
Search status: 98% ETTC 00:00:01
Search status: 99% ETTC 00:00:00
Search status: 100% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 92% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 49% ETTC 00:00:01
Search status: 93% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 74% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 98% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
== testthat results  ===========================================================
[ OK: 83 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 101.21    0.50  101.70

pqsfinder.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(testthat)
> library(pqsfinder)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

> 
> test_check("pqsfinder")
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
 compare pqsfinder_1_4_4_d, pqsfinder_1_4_4_r
 run default pqsfinder
Searching on sense strand...
Search status: finished              
 run pqsfinder using boost regex engine
Searching on sense strand...
Search status: finished              
 compare pv_d, pv_r
 compare pv_d, pqsfinder_1_4_4_d
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 30% ETTC 00:00:00
Search status: 43% ETTC 00:00:01
Search status: 46% ETTC 00:00:01
Search status: 47% ETTC 00:00:02
Search status: 48% ETTC 00:00:03
Search status: 49% ETTC 00:00:03
Search status: 55% ETTC 00:00:03
Search status: 59% ETTC 00:00:02
Search status: 78% ETTC 00:00:01
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 23% ETTC 00:00:00
Search status: 42% ETTC 00:00:00
Search status: 46% ETTC 00:00:01
Search status: 51% ETTC 00:00:00
Search status: 57% ETTC 00:00:00
Search status: 83% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 64% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 32% ETTC 00:00:00
Search status: 81% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 64% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 32% ETTC 00:00:00
Search status: 81% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 67% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 60% ETTC 00:00:00
Search status: 100% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 67% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 60% ETTC 00:00:00
Search status: 100% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 3% ETTC 00:00:00
Search status: 4% ETTC 00:00:24
Search status: 4% ETTC 00:01:12
Search status: 6% ETTC 00:00:47
Search status: 8% ETTC 00:00:46
Search status: 10% ETTC 00:00:45
Search status: 13% ETTC 00:00:40
Search status: 17% ETTC 00:00:34
Search status: 19% ETTC 00:00:34
Search status: 20% ETTC 00:00:36
Search status: 21% ETTC 00:00:37
Search status: 22% ETTC 00:00:42
Search status: 23% ETTC 00:00:43
Search status: 25% ETTC 00:00:42
Search status: 26% ETTC 00:00:45
Search status: 27% ETTC 00:00:45
Search status: 31% ETTC 00:00:40
Search status: 34% ETTC 00:00:34
Search status: 35% ETTC 00:00:37
Search status: 37% ETTC 00:00:35
Search status: 40% ETTC 00:00:33
Search status: 41% ETTC 00:00:33
Search status: 44% ETTC 00:00:30
Search status: 47% ETTC 00:00:27
Search status: 52% ETTC 00:00:23
Search status: 54% ETTC 00:00:22
Search status: 56% ETTC 00:00:21
Search status: 58% ETTC 00:00:20
Search status: 60% ETTC 00:00:19
Search status: 62% ETTC 00:00:18
Search status: 66% ETTC 00:00:15
Search status: 69% ETTC 00:00:14
Search status: 70% ETTC 00:00:14
Search status: 71% ETTC 00:00:13
Search status: 73% ETTC 00:00:12
Search status: 74% ETTC 00:00:13
Search status: 75% ETTC 00:00:12
Search status: 76% ETTC 00:00:12
Search status: 80% ETTC 00:00:10
Search status: 83% ETTC 00:00:08
Search status: 87% ETTC 00:00:06
Search status: 88% ETTC 00:00:05
Search status: 90% ETTC 00:00:04
Search status: 91% ETTC 00:00:04
Search status: 94% ETTC 00:00:02
Search status: 97% ETTC 00:00:01
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 92% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 49% ETTC 00:00:01
Search status: 93% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 74% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 98% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
== testthat results  ===========================================================
[ OK: 83 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  77.64    0.56   78.35

Example timings

pqsfinder.Rcheck/examples_i386/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.060.030.09
density-PQSViews-method0.040.000.03
maxScores-PQSViews-method0.020.000.01
maxScores000
pqsfinder0.030.000.03
score-PQSViews-method0.010.000.02
strand-PQSViews-method0.030.000.03

pqsfinder.Rcheck/examples_x64/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.080.000.08
density-PQSViews-method0.030.020.28
maxScores-PQSViews-method0.020.000.01
maxScores000
pqsfinder0.050.000.05
score-PQSViews-method0.010.000.01
strand-PQSViews-method0.030.000.03