##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DNABarcodes
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DNABarcodes’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DNABarcodes_init.c -o DNABarcodes_init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30,
from chromosome.h:8,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30,
from chromosome.h:8,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30,
from create_dnabarcodes.cpp:11:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from create_dnabarcodes.cpp:26:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template 