Package: DNABarcodes

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DNABarcodes_1.17.0.tar.gz

StartedAt: 2020-01-16 03:55:03 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:56:41 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 97.6 seconds

RetCode: 0

Status:  OK

CheckDir: DNABarcodes.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DNABarcodes_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DNABarcodes.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNABarcodes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DNABarcodes’ version ‘1.17.0’
* 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 ... OK
* 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
create.dnabarcodes 10.428  0.837   1.982
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/DNABarcodes.Rcheck/00check.log’
for details.

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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/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/vector:427:25: 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/clang8/bin/../include/c++/v1/vector:370:29: 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/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
        clear();
        ^
/usr/local/clang8/bin/../include/c++/v1/vector:496:5: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::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::__1::vector<Sequence, std::__1::allocator<Sequence> >::vector' requested here
  std::vector<Sequence> seqs;
                        ^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/vector:427:25: 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/clang8/bin/../include/c++/v1/vector:370:29: 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/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
        clear();
        ^
/usr/local/clang8/bin/../include/c++/v1/vector:496:5: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::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::__1::vector<Sequence, std::__1::allocator<Sequence> >::vector' requested here
  std::vector<Sequence> seqs;
                        ^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/vector:427:25: 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/clang8/bin/../include/c++/v1/vector:370:29: 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/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
        clear();
        ^
/usr/local/clang8/bin/../include/c++/v1/vector:558:5: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
    vector(const vector& __x);
    ^
chromosome.cpp:31:27: note: in instantiation of member function 'std::__1::vector<Sequence, std::__1::allocator<Sequence> >::vector' requested here
                          seed_(other.seed_), 
                          ^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1748:17: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
                __p->~_Tp();
                ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/__tree:1854:24: 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/clang8/bin/../include/c++/v1/__tree:1842:3: 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/clang8/bin/../include/c++/v1/set:442:28: note: in instantiation of member function 'std::__1::__tree<Sequence, std::__1::less<Sequence>, std::__1::allocator<Sequence> >::~__tree' requested here
class _LIBCPP_TEMPLATE_VIS set
                           ^
/usr/local/clang8/bin/../include/c++/v1/memory:1748:23: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/clang8/bin/../include/c++/v1/vector:275:
In file included from /usr/local/clang8/bin/../include/c++/v1/__bit_reference:16:
In file included from /usr/local/clang8/bin/../include/c++/v1/algorithm:644:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/vector:427:25: 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/clang8/bin/../include/c++/v1/vector:370:29: 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/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
        clear();
        ^
/usr/local/clang8/bin/../include/c++/v1/vector:558:5: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
    vector(const vector& __x);
    ^
conway.cpp:18:25: note: in instantiation of member function 'std::__1::vector<Sequence, std::__1::allocator<Sequence> >::vector' requested here
  std::vector<Sequence> code(seed);
                        ^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/vector:427:25: 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/clang8/bin/../include/c++/v1/vector:370:29: 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/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
        clear();
        ^
/usr/local/clang8/bin/../include/c++/v1/vector:496:5: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::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::__1::vector<Sequence, std::__1::allocator<Sequence> >::vector' requested here
  if (interrupt) return std::vector<Sequence>();
                        ^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/vector:427:25: 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/clang8/bin/../include/c++/v1/vector:370:29: 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/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
        clear();
        ^
/usr/local/clang8/bin/../include/c++/v1/vector:550:5: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::~__vector_base' requested here
    ~vector()
    ^
create_pool.cpp:25:32: note: in instantiation of member function 'std::__1::vector<Sequence, std::__1::allocator<Sequence> >::~vector' requested here
  std::vector<Sequence> pool = SequencePool::generate(n, filter_triplets, filter_gc, filter_self_complementary);
                               ^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1748:17: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
                __p->~_Tp();
                ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/__tree:1854:24: 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/clang8/bin/../include/c++/v1/__tree:1842:3: 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/clang8/bin/../include/c++/v1/set:442:28: note: in instantiation of member function 'std::__1::__tree<Sequence, std::__1::less<Sequence>, std::__1::allocator<Sequence> >::~__tree' requested here
class _LIBCPP_TEMPLATE_VIS set
                           ^
/usr/local/clang8/bin/../include/c++/v1/memory:1748:23: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'Sequence' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<Sequence>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/vector:427:25: 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/clang8/bin/../include/c++/v1/vector:370:29: 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/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::allocator<Sequence> >::clear' requested here
        clear();
        ^
/usr/local/clang8/bin/../include/c++/v1/vector:496:5: note: in instantiation of member function 'std::__1::__vector_base<Sequence, std::__1::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::__1::vector<Sequence, std::__1::allocator<Sequence> >::vector' requested here
  std::vector<Sequence> seqs;
                        ^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: 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/4.0/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)

name	user	system	elapsed
DNABarcodes-package	1.672	0.206	0.479
analyse.barcodes	0.076	0.066	0.036
barcode.set.distances	0.212	0.181	0.090
create.dnabarcodes	10.428	0.837	1.982
create.pool	0.210	0.230	0.102
demultiplex	2.997	0.725	3.663
distance	0.001	0.000	0.001