############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DNABarcodes ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘DNABarcodes’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++17 gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DNABarcodes_init.c -o DNABarcodes_init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c analyse_barcodes.cpp -o analyse_barcodes.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from analyse_barcodes.cpp:10: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from distance.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c barcode_set_distances.cpp -o barcode_set_distances.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from barcode_set_distances.cpp:10: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from distance.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c cachedistance.cpp -o cachedistance.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from cachedistance.cpp:7: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequence.h:13: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/numeric/ublas/matrix.hpp:18, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from cachedistance.cpp:8: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c chromosome.cpp -o chromosome.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from chromosome.cpp:3: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from distance.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from chromosome.h:17: genericchromosome.h: At global scope: genericchromosome.h:16:27: warning: ‘virtual bool GenericChromosome::operator<(const GenericChromosome&) const’ was hidden [-Woverloaded-virtual=] 16 | virtual bool operator<(const GenericChromosome&) const; | ^~~~~~~~ chromosome.h:49:27: note: by ‘virtual bool Chromosome::operator<(const Chromosome&) const’ 49 | virtual bool operator<(const Chromosome&) const; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from chromosome.cpp:15: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c code_falsification.cpp -o code_falsification.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from chromosome.h:6, from code_falsification.cpp:11: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from distance.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from chromosome.h:17: genericchromosome.h: At global scope: genericchromosome.h:16:27: warning: ‘virtual bool GenericChromosome::operator<(const GenericChromosome&) const’ was hidden [-Woverloaded-virtual=] 16 | virtual bool operator<(const GenericChromosome&) const; | ^~~~~~~~ chromosome.h:49:27: note: by ‘virtual bool Chromosome::operator<(const Chromosome&) const’ 49 | virtual bool operator<(const Chromosome&) const; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from code_falsification.cpp:26: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c conway.cpp -o conway.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from conway.h:8, from conway.cpp:3: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from distance.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from conway.cpp:11: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c create_distance_func.cpp -o create_distance_func.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from distance.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/numeric/ublas/matrix.hpp:18, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/numeric/ublas/symmetric.hpp:16, from cachedistance.h:16, from create_distance_func.cpp:9: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c create_dnabarcodes.cpp -o create_dnabarcodes.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from create_dnabarcodes.cpp:13: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_dnabarcodes.cpp:17: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/pointer_cast.hpp:13, from create_dnabarcodes.cpp:14: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from greedyevolution.h:9, from create_dnabarcodes.cpp:23: genericchromosome.h: At global scope: genericchromosome.h:16:27: warning: ‘virtual bool GenericChromosome::operator<(const GenericChromosome&) const’ was hidden [-Woverloaded-virtual=] 16 | virtual bool operator<(const GenericChromosome&) const; | ^~~~~~~~ In file included from create_dnabarcodes.cpp:25: chromosome.h:49:27: note: by ‘virtual bool Chromosome::operator<(const Chromosome&) const’ 49 | virtual bool operator<(const Chromosome&) const; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:22, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from create_dnabarcodes.cpp:26: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) noexcept : px( p.release() ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c create_pool.cpp -o create_pool.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from create_pool.cpp:6: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from create_pool.cpp:12: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequence.h:13: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c demultiplex.cpp -o demultiplex.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from demultiplex.cpp:9: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from distance.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c distance_for_R.cpp -o distance_for_R.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from distance.h:11: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c genericchromosome.cpp -o genericchromosome.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c greedyevolution.cpp -o greedyevolution.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from greedyevolution.h:8, from greedyevolution.cpp:5: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequence.h:13: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from greedyevolution.cpp:12: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c hammingdistance.cpp -o hammingdistance.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from hammingdistance.cpp:7: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequence.h:13: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c helpers.cpp -o helpers.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c levenshteindistance.cpp -o levenshteindistance.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from levenshteindistance.cpp:7: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequence.h:13: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:22, from maxclique.h:12, from maxclique_pattabiraman_heuristic.h:10, from maxclique_pattabiraman_heuristic.cpp:6: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) noexcept : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/unordered/detail/opt_storage.hpp:11, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/unordered/detail/archive_constructed.hpp:12, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/unordered/detail/serialize_container.hpp:14, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/unordered/detail/serialize_fca_container.hpp:12, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:18, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/graph/graph_traits.hpp:25, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:24: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c phaseshiftdist.cpp -o phaseshiftdist.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from phaseshiftdist.cpp:10: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequence.h:13: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from phaseshiftdist.cpp:23: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sequence.cpp -o sequence.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from sequence.cpp:3: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequence.cpp:13: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequence.cpp:10: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from sequencelevenshteindistance.cpp:3: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequence.h:13: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sequencepool.cpp -o sequencepool.o In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from sequence.h:19, from distance.h:14, from sequencepool.cpp:11: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from sequencepool.cpp:9: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/foreach.hpp:76, from sequencepool.cpp:16: /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o DNABarcodes.so DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -fopenmp -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-DNABarcodes/00new/DNABarcodes/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** 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 (DNABarcodes)