############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL DNABarcodes ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'DNABarcodes' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DNABarcodes_init.c -o DNABarcodes_init.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c analyse_barcodes.cpp -o analyse_barcodes.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from analyse_barcodes.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from analyse_barcodes.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from analyse_barcodes.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from analyse_barcodes.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from analyse_barcodes.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from analyse_barcodes.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from analyse_barcodes.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c barcode_set_distances.cpp -o barcode_set_distances.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from barcode_set_distances.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from barcode_set_distances.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from barcode_set_distances.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from barcode_set_distances.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from barcode_set_distances.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from barcode_set_distances.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from barcode_set_distances.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cachedistance.cpp -o cachedistance.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/serialization/array.hpp:26, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from cachedistance.cpp:8: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromosome.cpp -o chromosome.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from chromosome.h:6, from chromosome.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from chromosome.h:6, from chromosome.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from chromosome.h:6, from chromosome.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from chromosome.h:6, from chromosome.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from chromosome.h:6, from chromosome.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from chromosome.h:6, from chromosome.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from chromosome.h:6, from chromosome.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from chromosome.cpp:15: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c code_falsification.cpp -o code_falsification.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from code_falsification.cpp:5: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from code_falsification.cpp:5: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from code_falsification.cpp:5: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from code_falsification.cpp:5: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from code_falsification.cpp:5: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from code_falsification.cpp:5: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from code_falsification.cpp:5: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from code_falsification.cpp:26: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c conway.cpp -o conway.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from conway.h:8, from conway.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from conway.h:8, from conway.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from conway.h:8, from conway.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from conway.h:8, from conway.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from conway.h:8, from conway.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from conway.h:8, from conway.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance.h:8, from conway.h:8, from conway.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from conway.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_distance_func.cpp -o create_distance_func.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/serialization/array.hpp:26, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from create_distance_func.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_dnabarcodes.cpp -o create_dnabarcodes.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from create_dnabarcodes.cpp:13: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_dnabarcodes.cpp:17: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_dnabarcodes.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_dnabarcodes.cpp:17: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_dnabarcodes.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_dnabarcodes.cpp:17: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_dnabarcodes.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_dnabarcodes.cpp:17: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_dnabarcodes.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_dnabarcodes.cpp:17: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_dnabarcodes.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_dnabarcodes.cpp:17: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_dnabarcodes.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_dnabarcodes.cpp:17: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_dnabarcodes.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from create_dnabarcodes.cpp:26: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_dnabarcodes.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_pool.cpp -o create_pool.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from create_pool.cpp:6: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_pool.cpp:12: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_pool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_pool.cpp:12: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_pool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_pool.cpp:12: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_pool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_pool.cpp:12: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_pool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_pool.cpp:12: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_pool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_pool.cpp:12: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_pool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_pool.cpp:12: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_pool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c demultiplex.cpp -o demultiplex.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from demultiplex.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from demultiplex.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from demultiplex.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from demultiplex.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from demultiplex.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from demultiplex.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from demultiplex.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from demultiplex.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from demultiplex.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from demultiplex.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from demultiplex.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from demultiplex.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from demultiplex.cpp:9: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from demultiplex.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distance_for_R.cpp -o distance_for_R.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance_for_R.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance_for_R.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance_for_R.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance_for_R.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance_for_R.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance_for_R.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from distance_for_R.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genericchromosome.cpp -o genericchromosome.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c greedyevolution.cpp -o greedyevolution.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from greedyevolution.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from greedyevolution.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from greedyevolution.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from greedyevolution.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from greedyevolution.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from greedyevolution.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from greedyevolution.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from greedyevolution.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hammingdistance.cpp -o hammingdistance.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from hammingdistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from hammingdistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from hammingdistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from hammingdistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from hammingdistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from hammingdistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from hammingdistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c helpers.cpp -o helpers.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c levenshteindistance.cpp -o levenshteindistance.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from levenshteindistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from levenshteindistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from levenshteindistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from levenshteindistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from levenshteindistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from levenshteindistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from levenshteindistance.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from maxclique_pattabiraman_heuristic.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25, from F:/biocbuild/bbs-3.16-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: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598, from F:/biocbuild/bbs-3.16-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: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from maxclique_pattabiraman_heuristic.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598, from F:/biocbuild/bbs-3.16-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: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from maxclique_pattabiraman_heuristic.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598, from F:/biocbuild/bbs-3.16-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: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from maxclique_pattabiraman_heuristic.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598, from F:/biocbuild/bbs-3.16-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: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from maxclique_pattabiraman_heuristic.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598, from F:/biocbuild/bbs-3.16-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: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from maxclique_pattabiraman_heuristic.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598, from F:/biocbuild/bbs-3.16-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: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from maxclique_pattabiraman_heuristic.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598, from F:/biocbuild/bbs-3.16-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: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from maxclique_pattabiraman_heuristic.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c phaseshiftdist.cpp -o phaseshiftdist.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from phaseshiftdist.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from phaseshiftdist.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from phaseshiftdist.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from phaseshiftdist.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from phaseshiftdist.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from phaseshiftdist.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from phaseshiftdist.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from phaseshiftdist.cpp:23: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequence.cpp -o sequence.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from sequence.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.cpp:10: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.cpp:10: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.cpp:10: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.cpp:10: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.cpp:10: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.cpp:10: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.cpp:10: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.h:13, from sequencelevenshteindistance.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.h:13, from sequencelevenshteindistance.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.h:13, from sequencelevenshteindistance.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.h:13, from sequencelevenshteindistance.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.h:13, from sequencelevenshteindistance.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.h:13, from sequencelevenshteindistance.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83, from sequence.h:13, from sequencelevenshteindistance.cpp:3: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequencepool.cpp -o sequencepool.o In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from sequencepool.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from sequencepool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from sequencepool.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from sequencepool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from sequencepool.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from sequencepool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from sequencepool.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from sequencepool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from sequencepool.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from sequencepool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from sequencepool.cpp:11: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from sequencepool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from sequencepool.cpp:11: F:/biocbuild/bbs-3.16-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>&&)': F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43, from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53, from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27, from sequencepool.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/foreach.hpp:76, from sequencepool.cpp:16: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-DNABarcodes/00new/DNABarcodes/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DNABarcodes)