############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/pqsfinder_2.8.0.tar.gz && rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pqsfinder.buildbin-libdir pqsfinder_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pqsfinder_2.8.0.zip && rm pqsfinder_2.8.0.tar.gz pqsfinder_2.8.0.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 107k 100 107k 0 0 457k 0 --:--:-- --:--:-- --:--:-- 459k 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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ pqsfinder.cpp: In function 'void find_all_runs(SEXP, int, std::__cxx11::basic_string::const_iterator, std::__cxx11::basic_string::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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( 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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ mkdir -p "C:/Users/biocbuild/bbs-3.13-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386" "C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.13-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-3.13-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-3.13-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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( 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-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ pqsfinder.cpp: In function 'void find_all_runs(SEXP, int, std::__cxx11::basic_string::const_iterator, std::__cxx11::basic_string::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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && 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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( 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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template 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-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ mkdir -p "C:/Users/biocbuild/bbs-3.13-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64" "C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'pqsfinder' as pqsfinder_2.8.0.zip * DONE (pqsfinder) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'pqsfinder' successfully unpacked and MD5 sums checked