DNABarcodes 1.16.0
Tilo Buschmann
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/DNABarcodes |
| Branch: RELEASE_3_10 |
| Last Commit: 24c7d1e |
| Last Changed Date: 2019-10-29 13:09:26 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | [ OK ] | OK | OK | OK | |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DNABarcodes
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DNABarcodes’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c DNABarcodes_init.c -o DNABarcodes_init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c analyse_barcodes.cpp -o analyse_barcodes.o
In file included from analyse_barcodes.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::destroy<Sequence>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
clear();
^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c barcode_set_distances.cpp -o barcode_set_distances.o
In file included from barcode_set_distances.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::destroy<Sequence>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
clear();
^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c cachedistance.cpp -o cachedistance.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c chromosome.cpp -o chromosome.o
In file included from chromosome.cpp:3:
In file included from ./chromosome.h:6:
In file included from ./distance.h:8:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::destroy<Sequence>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
clear();
^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c code_falsification.cpp -o code_falsification.o
In file included from code_falsification.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1733:17: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
__p->~_Tp();
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::__tree_node<Sequence, void *> > >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/__tree:1863:24: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::__tree_node<Sequence, void *> > >::destroy<Sequence>' requested here
__node_traits::destroy(__na, _NodeTypes::__get_ptr(__nd->__value_));
^
/usr/local/clang7/include/c++/v1/__tree:1851:3: note: in instantiation of member function 'std::__1::__tree<Sequence, std::__1::less<Sequence>, std::__1::allocator<Sequence> >::destroy' requested here
destroy(__root());
^
/usr/local/clang7/include/c++/v1/__tree:879:70: note: in instantiation of member function 'std::__1::__tree<Sequence, std::__1::less<Sequence>, std::__1::allocator<Sequence> >::~__tree' requested here
template <class, class, class> friend class _LIBCPP_TEMPLATE_VIS set;
^
/usr/local/clang7/include/c++/v1/memory:1733:23: note: qualify call to silence this warning
__p->~_Tp();
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c conway.cpp -o conway.o
In file included from conway.cpp:3:
In file included from ./conway.h:6:
In file included from /usr/local/clang7/include/c++/v1/vector:270:
In file included from /usr/local/clang7/include/c++/v1/__bit_reference:15:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::destroy<Sequence>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
clear();
^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c create_distance_func.cpp -o create_distance_func.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from create_dnabarcodes.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::destroy<Sequence>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
clear();
^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c create_pool.cpp -o create_pool.o
In file included from create_pool.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::destroy<Sequence>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
clear();
^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c demultiplex.cpp -o demultiplex.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c distance_for_R.cpp -o distance_for_R.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c genericchromosome.cpp -o genericchromosome.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c greedyevolution.cpp -o greedyevolution.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c hammingdistance.cpp -o hammingdistance.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c helpers.cpp -o helpers.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c levenshteindistance.cpp -o levenshteindistance.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c phaseshiftdist.cpp -o phaseshiftdist.o
In file included from phaseshiftdist.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1733:17: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
__p->~_Tp();
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::__tree_node<Sequence, void *> > >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/__tree:1863:24: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::__tree_node<Sequence, void *> > >::destroy<Sequence>' requested here
__node_traits::destroy(__na, _NodeTypes::__get_ptr(__nd->__value_));
^
/usr/local/clang7/include/c++/v1/__tree:1851:3: note: in instantiation of member function 'std::__1::__tree<Sequence, std::__1::less<Sequence>, std::__1::allocator<Sequence> >::destroy' requested here
destroy(__root());
^
/usr/local/clang7/include/c++/v1/__tree:879:70: note: in instantiation of member function 'std::__1::__tree<Sequence, std::__1::less<Sequence>, std::__1::allocator<Sequence> >::~__tree' requested here
template <class, class, class> friend class _LIBCPP_TEMPLATE_VIS set;
^
/usr/local/clang7/include/c++/v1/memory:1733:23: note: qualify call to silence this warning
__p->~_Tp();
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c sequence.cpp -o sequence.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c sequencepool.cpp -o sequencepool.o
In file included from sequencepool.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::__destroy<Sequence>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<Sequence> >::destroy<Sequence>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
clear();
^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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)