############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DNABarcodes_1.22.0.tar.gz && rm -rf DNABarcodes.buildbin-libdir && mkdir DNABarcodes.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DNABarcodes.buildbin-libdir DNABarcodes_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DNABarcodes_1.22.0.zip && rm DNABarcodes_1.22.0.tar.gz DNABarcodes_1.22.0.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 129k 100 129k 0 0 679k 0 --:--:-- --:--:-- --:--:-- 681k install for i386 * installing *source* package 'DNABarcodes' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -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" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DNABarcodes_init.c -o DNABarcodes_init.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c analyse_barcodes.cpp -o analyse_barcodes.o 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c barcode_set_distances.cpp -o barcode_set_distances.o In file included from C:/Users/biocbuild/bbs-3.13-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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cachedistance.cpp -o cachedistance.o 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from cachedistance.cpp:8: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromosome.cpp -o chromosome.o 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: 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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from chromosome.cpp:15: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c code_falsification.cpp -o code_falsification.o 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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/foreach.hpp:76, from code_falsification.cpp:26: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c conway.cpp -o conway.o 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 sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: 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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from conway.cpp:11: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_distance_func.cpp -o create_distance_func.o In file included from C:/Users/biocbuild/bbs-3.13-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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from create_distance_func.cpp:9: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_dnabarcodes.cpp -o create_dnabarcodes.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from create_dnabarcodes.cpp:13: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from create_dnabarcodes.cpp:26: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: 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 create_dnabarcodes.cpp:3: 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/graph/adjacency_iterator.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from create_dnabarcodes.cpp:26: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead. BOOST_HEADER_DEPRECATED("") ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_pool.cpp -o create_pool.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from create_pool.cpp:6: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c demultiplex.cpp -o demultiplex.o 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distance_for_R.cpp -o distance_for_R.o In file included from C:/Users/biocbuild/bbs-3.13-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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genericchromosome.cpp -o genericchromosome.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c greedyevolution.cpp -o greedyevolution.o 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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/foreach.hpp:76, from greedyevolution.cpp:11: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hammingdistance.cpp -o hammingdistance.o 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c helpers.cpp -o helpers.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c levenshteindistance.cpp -o levenshteindistance.o 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/graph/adjacency_iterator.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead. BOOST_HEADER_DEPRECATED("") ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c phaseshiftdist.cpp -o phaseshiftdist.o 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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/foreach.hpp:76, from phaseshiftdist.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequence.cpp -o sequence.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from sequence.cpp:3: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o 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 sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequencepool.cpp -o sequencepool.o 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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/foreach.hpp:76, from sequencepool.cpp:16: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DNABarcodes.dll tmp.def DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -fopenmp -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DNABarcodes.buildbin-libdir/00LOCK-DNABarcodes/00new/DNABarcodes/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'DNABarcodes' finding HTML links ... done DNABarcodes-package html analyse.barcodes html barcode.set.distances html create.dnabarcodes html create.pool html demultiplex html distance html mutatedReads html supplierSet html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'DNABarcodes' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DNABarcodes_init.c -o DNABarcodes_init.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c analyse_barcodes.cpp -o analyse_barcodes.o 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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 sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: 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 analyse_barcodes.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c barcode_set_distances.cpp -o barcode_set_distances.o In file included from C:/Users/biocbuild/bbs-3.13-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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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 sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: 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 barcode_set_distances.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cachedistance.cpp -o cachedistance.o 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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 sequence.h:19, from cachedistance.cpp:7: 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 cachedistance.cpp:4: 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/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from cachedistance.cpp:8: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromosome.cpp -o chromosome.o 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: 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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from chromosome.h:6, from chromosome.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from chromosome.cpp:15: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c code_falsification.cpp -o code_falsification.o 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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 sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: 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 code_falsification.cpp:5: 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/foreach.hpp:76, from code_falsification.cpp:26: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c conway.cpp -o conway.o 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 sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: 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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: C:/Users/biocbuild/bbs-3.13-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 distance.h:8, from conway.h:8, from conway.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from conway.cpp:11: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_distance_func.cpp -o create_distance_func.o In file included from C:/Users/biocbuild/bbs-3.13-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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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 sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: 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 create_distance_func.cpp:3: 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/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/serialization/array.hpp:26, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from create_distance_func.cpp:9: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_dnabarcodes.cpp -o create_dnabarcodes.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from create_dnabarcodes.cpp:13: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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 sequence.h:19, from create_dnabarcodes.cpp:17: 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 create_dnabarcodes.cpp:3: 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/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from create_dnabarcodes.cpp:26: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: 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 create_dnabarcodes.cpp:3: 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/graph/adjacency_iterator.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from create_dnabarcodes.cpp:26: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead. BOOST_HEADER_DEPRECATED("") ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_pool.cpp -o create_pool.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from create_pool.cpp:6: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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 sequence.h:19, from create_pool.cpp:12: 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 create_pool.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c demultiplex.cpp -o demultiplex.o 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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 sequence.h:19, from distance.h:14, from demultiplex.cpp:9: 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 demultiplex.cpp:3: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distance_for_R.cpp -o distance_for_R.o In file included from C:/Users/biocbuild/bbs-3.13-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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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 sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: 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 distance_for_R.cpp:3: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genericchromosome.cpp -o genericchromosome.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c greedyevolution.cpp -o greedyevolution.o 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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 sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: 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 greedyevolution.cpp:3: 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/foreach.hpp:76, from greedyevolution.cpp:11: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hammingdistance.cpp -o hammingdistance.o 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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 sequence.h:19, from hammingdistance.cpp:7: 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 hammingdistance.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c helpers.cpp -o helpers.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c levenshteindistance.cpp -o levenshteindistance.o 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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 sequence.h:19, from levenshteindistance.cpp:7: 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 levenshteindistance.cpp:4: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-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 maxclique_pattabiraman_heuristic.cpp:4: 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/graph/adjacency_iterator.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead. BOOST_HEADER_DEPRECATED("") ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c phaseshiftdist.cpp -o phaseshiftdist.o 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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 sequence.h:19, from phaseshiftdist.cpp:10: 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 phaseshiftdist.cpp:4: 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/foreach.hpp:76, from phaseshiftdist.cpp:23: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequence.cpp -o sequence.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76, from sequence.cpp:3: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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 sequence.h:19, from sequence.cpp:13: 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 sequence.cpp:10: 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o 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 sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: 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 sequence.h:13, from sequencelevenshteindistance.cpp:3: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequencepool.cpp -o sequencepool.o 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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 sequence.h:19, from distance.h:14, from sequencepool.cpp:11: 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 sequencepool.cpp:4: 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/foreach.hpp:76, from sequencepool.cpp:16: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DNABarcodes.dll tmp.def DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DNABarcodes.buildbin-libdir/DNABarcodes/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'DNABarcodes' as DNABarcodes_1.22.0.zip * DONE (DNABarcodes) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'DNABarcodes' successfully unpacked and MD5 sums checked