##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DNABarcodes_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DNABarcodes.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 13.0.0 (clang-1300.0.29.3)
    GNU Fortran (GCC) 12.0.1 20220312 (experimental)
* running under: macOS Monterey 12.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNABarcodes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DNABarcodes’ version ‘1.29.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DNABarcodes’ can be installed ... WARNING
Found the following significant warnings:
  greedyevolution.cpp:83:10: warning: 'random_shuffle<std::__wrap_iter<boost::shared_ptr<GenericChromosome> *>, int (&)(int)>' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DNABarcodes.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX13.0.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    First development version for introduction to Bioconductor
  Cannot process chunk/lines:
    This is the first public release.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analyse.barcodes : <anonymous>: no visible global function definition
  for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DNABarcodes.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DNABarcodes
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘DNABarcodes’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX13.0.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DNABarcodes_init.c -o DNABarcodes_init.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:22:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<Sequence>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<Sequence>>::destroy<Sequence, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:519:5: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::~__vector_base' requested here
    vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
    ^
analyse_barcodes.cpp:33:25: note: in instantiation of member function 'std::vector<Sequence>::vector' requested here
  std::vector<Sequence> seqs;
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:22:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<Sequence>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<Sequence>>::destroy<Sequence, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:519:5: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::~__vector_base' requested here
    vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
    ^
barcode_set_distances.cpp:31:25: note: in instantiation of member function 'std::vector<Sequence>::vector' requested here
  std::vector<Sequence> seqs;
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cachedistance.cpp -o cachedistance.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:22:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<Sequence>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<Sequence>>::destroy<Sequence, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:581:5: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::~__vector_base' requested here
    vector(const vector& __x);
    ^
chromosome.cpp:31:27: note: in instantiation of member function 'std::vector<Sequence>::vector' requested here
                          seed_(other.seed_), 
                          ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:319:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__tree:1803:24: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::__tree_node<Sequence, void *>>>::destroy<Sequence, void, void>' requested here
        __node_traits::destroy(__na, _NodeTypes::__get_ptr(__nd->__value_));
                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__tree:1791:3: note: in instantiation of member function 'std::__tree<Sequence, std::less<Sequence>, std::allocator<Sequence>>::destroy' requested here
  destroy(__root());
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/set:502:5: note: in instantiation of member function 'std::__tree<Sequence, std::less<Sequence>, std::allocator<Sequence>>::~__tree' requested here
    set()
    ^
code_falsification.cpp:41:22: note: in instantiation of member function 'std::set<Sequence>::set' requested here
  std::set<Sequence> all_new_mutations;
                     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:319:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:275:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:22:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<Sequence>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<Sequence>>::destroy<Sequence, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:581:5: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::~__vector_base' requested here
    vector(const vector& __x);
    ^
conway.cpp:18:25: note: in instantiation of member function 'std::vector<Sequence>::vector' requested here
  std::vector<Sequence> code(seed);
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c create_distance_func.cpp -o create_distance_func.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from create_dnabarcodes.cpp:26:
In file included from ./maxclique_pattabiraman_heuristic.h:10:
In file included from ./maxclique.h:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
./maxclique_pattabiraman_heuristic.h:27:32: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS>>' requested here
                typedef boost::graph_traits< MaxClique::Graph >::out_edge_iterator out_edge_iterator_t;
                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from create_dnabarcodes.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:22:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<Sequence>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<Sequence>>::destroy<Sequence, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:519:5: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::~__vector_base' requested here
    vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
    ^
create_dnabarcodes.cpp:72:25: note: in instantiation of member function 'std::vector<Sequence>::vector' requested here
  if (interrupt) return std::vector<Sequence>();
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:22:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<Sequence>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<Sequence>>::destroy<Sequence, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:573:5: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::~__vector_base' requested here
    ~vector()
    ^
create_pool.cpp:25:32: note: in instantiation of member function 'std::vector<Sequence>::~vector' requested here
  std::vector<Sequence> pool = SequencePool::generate(n, filter_triplets, filter_gc, filter_self_complementary);
                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c demultiplex.cpp -o demultiplex.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c distance_for_R.cpp -o distance_for_R.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c genericchromosome.cpp -o genericchromosome.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c greedyevolution.cpp -o greedyevolution.o
greedyevolution.cpp:83:10: warning: 'random_shuffle<std::__wrap_iter<boost::shared_ptr<GenericChromosome> *>, int (&)(int)>' is deprecated [-Wdeprecated-declarations]
    std::random_shuffle(chromosomes.begin(), chromosomes.end(), randWrapper);
         ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/shuffle.h:81:1: note: 'random_shuffle<std::__wrap_iter<boost::shared_ptr<GenericChromosome> *>, int (&)(int)>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX14 void
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1060:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14'
#  define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hammingdistance.cpp -o hammingdistance.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c helpers.cpp -o helpers.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c levenshteindistance.cpp -o levenshteindistance.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
In file included from maxclique_pattabiraman_heuristic.cpp:6:
In file included from ./maxclique_pattabiraman_heuristic.h:10:
In file included from ./maxclique.h:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/scoped_ptr.hpp:13:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr m_property;
                 ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS>' requested here
    typedef typename G::vertex_descriptor vertex_descriptor;
                     ^
./maxclique_pattabiraman_heuristic.h:27:32: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS>>' requested here
                typedef boost::graph_traits< MaxClique::Graph >::out_edge_iterator out_edge_iterator_t;
                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:319:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__tree:1803:24: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::__tree_node<Sequence, void *>>>::destroy<Sequence, void, void>' requested here
        __node_traits::destroy(__na, _NodeTypes::__get_ptr(__nd->__value_));
                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__tree:1791:3: note: in instantiation of member function 'std::__tree<Sequence, std::less<Sequence>, std::allocator<Sequence>>::destroy' requested here
  destroy(__root());
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/set:502:5: note: in instantiation of member function 'std::__tree<Sequence, std::less<Sequence>, std::allocator<Sequence>>::~__tree' requested here
    set()
    ^
phaseshiftdist.cpp:129:22: note: in instantiation of member function 'std::set<Sequence>::set' requested here
  std::set<Sequence> already_seen;
                     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:319:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sequence.cpp -o sequence.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:22:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:9: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
        __p->~_Tp();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<Sequence>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<Sequence>>::destroy<Sequence, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:519:5: note: in instantiation of member function 'std::__vector_base<Sequence, std::allocator<Sequence>>::~__vector_base' requested here
    vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
    ^
sequencepool.cpp:23:25: note: in instantiation of member function 'std::vector<Sequence>::vector' requested here
  std::vector<Sequence> seqs;
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: qualify call to silence this warning
        __p->~_Tp();
              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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)