############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf DNABarcodeCompatibility.buildbin-libdir && mkdir DNABarcodeCompatibility.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=DNABarcodeCompatibility.buildbin-libdir DNABarcodeCompatibility_1.23.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'DNABarcodeCompatibility' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DNABarcodes_init.c -o DNABarcodes_init.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cachedistance.cpp -o cachedistance.o cachedistance.cpp:51: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 51 | #pragma omp critical | cachedistance.cpp:66: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 66 | #pragma omp critical | In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78, from sequence.h:13: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array.hpp:26, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from cachedistance.cpp:8: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ | - E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ | - In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/traits.hpp:21, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:27: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 111 | public std::iterator { | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_algobase.h:65, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\specfun.h:43, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\cmath:3699, from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:100, from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66, from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/RcppCommon.h:30, from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 149 | public std::iterator { | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 204 | public std::iterator { | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_distance_func.cpp -o create_distance_func.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78, from distance.h:11: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array_optimization.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array_wrapper.hpp:21, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/serialization/array.hpp:26, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:22, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/vector.hpp:21, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/matrix.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from create_distance_func.cpp:9: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ | - E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ | - In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/traits.hpp:21, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/storage.hpp:27: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 111 | public std::iterator { | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_algobase.h:65, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\specfun.h:43, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\cmath:3699, from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:100, from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66, from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/RcppCommon.h:30, from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 149 | public std::iterator { | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 204 | public std::iterator { | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distance_for_R.cpp -o distance_for_R.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78, from distance.h:11: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hammingdistance.cpp -o hammingdistance.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78, from sequence.h:13: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c levenshteindistance.cpp -o levenshteindistance.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78, from sequence.h:13: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c phaseshiftdist.cpp -o phaseshiftdist.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78, from sequence.h:13: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76, from phaseshiftdist.cpp:23: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ | - E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ | - g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequence.cpp -o sequence.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/foreach.hpp:76, from sequence.cpp:3: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ | - E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ | - In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78, from sequence.cpp:10: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78, from sequence.h:13: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o DNABarcodeCompatibility.dll tmp.def DNABarcodes_init.o RcppExports.o cachedistance.o create_distance_func.o distance_for_R.o hammingdistance.o levenshteindistance.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/meat/DNABarcodeCompatibility.buildbin-libdir/00LOCK-DNABarcodeCompatibility/00new/DNABarcodeCompatibility/libs/x64 ** R ** data *** moving datasets to lazyload DB ** 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 * MD5 sums packaged installation of 'DNABarcodeCompatibility' as DNABarcodeCompatibility_1.23.0.zip * DONE (DNABarcodeCompatibility)