############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DNABarcodeCompatibility ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘DNABarcodeCompatibility’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c DNABarcodes_init.c -o DNABarcodes_init.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -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 /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from sequence.h:13: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-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 ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/matrix.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from cachedistance.cpp:8: /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ | - /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/traits.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/storage.hpp:27: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_algobase.h:65, from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/specfun.h:43, from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/cmath:3898, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/platform/compiler.h:100, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/r/headers.h:66, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:30, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27, from cachedistance.cpp:4: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 149 | public std::iterator { | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 204 | public std::iterator { | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c create_distance_func.cpp -o create_distance_func.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from create_distance_func.cpp:5: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from distance.h:11: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-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 ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/matrix.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from create_distance_func.cpp:9: /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ | - /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/traits.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/storage.hpp:27: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_algobase.h:65, from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/specfun.h:43, from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/cmath:3898, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/platform/compiler.h:100, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/r/headers.h:66, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:30, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27, from create_distance_func.cpp:3: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 149 | public std::iterator { | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 204 | public std::iterator { | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c distance_for_R.cpp -o distance_for_R.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from distance_for_R.cpp:9: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from distance.h:11: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-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 ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c hammingdistance.cpp -o hammingdistance.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from sequence.h:13: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-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 ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c levenshteindistance.cpp -o levenshteindistance.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from sequence.h:13: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-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 ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c phaseshiftdist.cpp -o phaseshiftdist.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from sequence.h:13: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-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 ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/foreach.hpp:76, from phaseshiftdist.cpp:23: /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ | - /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ /home/biocbuild/R/R-4.4.1/site-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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c sequence.cpp -o sequence.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/foreach.hpp:76, from sequence.cpp:3: /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ | - /home/biocbuild/R/R-4.4.1/site-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 | ); | ~ /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from sequence.cpp:10: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-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 ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from sequence.h:13: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-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 ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o DNABarcodeCompatibility.so 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 -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-DNABarcodeCompatibility/00new/DNABarcodeCompatibility/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DNABarcodeCompatibility)