* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘DNAtools’ ...
** this is package ‘DNAtools’ version ‘0.2-5’
** package ‘DNAtools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 21.1.8 (3)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5T6Fuq/R.INSTALL265f5b4e61ee/DNAtools/src'
clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c class_DNTRare.cpp -o class_DNTRare.o
clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c compare-utils.cpp -o compare-utils.o
compare-utils.cpp:107:20: warning: object backing the pointer will be destroyed at the end of the full-expression [-Wdangling-gsl]
107 | int *pnProf1 = &(Rcpp::as<std::vector<int> >(prof1)[0]); // this should replace INTEGER(prof1)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compare-utils.cpp:108:20: warning: object backing the pointer will be destroyed at the end of the full-expression [-Wdangling-gsl]
108 | int *pnProf2 = &(Rcpp::as<std::vector<int> >(prof2)[0]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2 warnings generated.
clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c compare.cpp -o compare.o
clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c compare_threaded.cpp -o compare_threaded.o
In file included from compare_threaded.cpp:14:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/RcppParallel.h:24:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:11:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/concurrent_unordered_set.h:23:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:37:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile long long' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<long long>::converter<const volatile long long>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile long long]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:434:1: note: in instantiation of member function 'tbb::internal::atomic_impl<long long>::operator long long' requested here
434 | __TBB_DECL_ATOMIC(__TBB_LONG_LONG)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile unsigned long long' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<unsigned long long>::converter<const volatile unsigned long long>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile unsigned long long]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:435:1: note: in instantiation of member function 'tbb::internal::atomic_impl<unsigned long long>::operator unsigned long long' requested here
435 | __TBB_DECL_ATOMIC(unsigned __TBB_LONG_LONG)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile long' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<long>::converter<const volatile long>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile long]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:439:1: note: in instantiation of member function 'tbb::internal::atomic_impl<long>::operator long' requested here
439 | __TBB_DECL_ATOMIC(long)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile unsigned long' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<unsigned long>::converter<const volatile unsigned long>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile unsigned long]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:440:1: note: in instantiation of member function 'tbb::internal::atomic_impl<unsigned long>::operator unsigned long' requested here
440 | __TBB_DECL_ATOMIC(unsigned long)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile unsigned int' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<unsigned int>::converter<const volatile unsigned int>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile unsigned int]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:466:1: note: in instantiation of member function 'tbb::internal::atomic_impl<unsigned int>::operator unsigned int' requested here
466 | __TBB_DECL_ATOMIC(unsigned)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile int' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<int>::converter<const volatile int>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile int]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:467:1: note: in instantiation of member function 'tbb::internal::atomic_impl<int>::operator int' requested here
467 | __TBB_DECL_ATOMIC(int)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile unsigned short' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<unsigned short>::converter<const volatile unsigned short>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile unsigned short]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:470:1: note: in instantiation of member function 'tbb::internal::atomic_impl<unsigned short>::operator unsigned short' requested here
470 | __TBB_DECL_ATOMIC(unsigned short)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile short' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<short>::converter<const volatile short>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile short]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:471:1: note: in instantiation of member function 'tbb::internal::atomic_impl<short>::operator short' requested here
471 | __TBB_DECL_ATOMIC(short)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile char' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<char>::converter<const volatile char>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile char]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:472:1: note: in instantiation of member function 'tbb::internal::atomic_impl<char>::operator char' requested here
472 | __TBB_DECL_ATOMIC(char)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile signed char' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<signed char>::converter<const volatile signed char>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile signed char]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:473:1: note: in instantiation of member function 'tbb::internal::atomic_impl<signed char>::operator signed char' requested here
473 | __TBB_DECL_ATOMIC(signed char)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile unsigned char' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<unsigned char>::converter<const volatile unsigned char>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile unsigned char]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:474:1: note: in instantiation of member function 'tbb::internal::atomic_impl<unsigned char>::operator unsigned char' requested here
474 | __TBB_DECL_ATOMIC(unsigned char)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile wchar_t' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<wchar_t>::converter<const volatile wchar_t>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile wchar_t]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:477:1: note: in instantiation of member function 'tbb::internal::atomic_impl<wchar_t>::operator wchar_t' requested here
477 | __TBB_DECL_ATOMIC(wchar_t)
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:422:78: note: expanded from macro '__TBB_DECL_ATOMIC'
422 | atomic<T>& operator=( const atomic<T>& rhs ) {store_with_release(rhs); return *this;} \
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'void *const volatile' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<void *>::converter<void *const volatile>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = void *const volatile]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:509:34: note: in instantiation of member function 'tbb::internal::atomic_impl<void *>::operator void *' requested here
509 | this->store_with_release(rhs); return *this;
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:226:18: warning: volatile-qualified parameter type 'const volatile bool' is deprecated [-Wdeprecated-volatile]
226 | converter(value_type a_value) : value(a_value) {}
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:255:21: note: in instantiation of template class 'tbb::internal::atomic_impl<bool>::converter<const volatile bool>' requested here
255 | static typename converter<value_t>::bits_type & to_bits_ref(value_t& value){
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/internal/../atomic.h:297:42: note: while substituting deduced template arguments into function template 'to_bits_ref' [with value_t = const volatile bool]
297 | __TBB_load_with_acquire( to_bits_ref(my_storage.my_value) )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/partitioner.h:140:16: note: in instantiation of member function 'tbb::internal::atomic_impl<bool>::operator bool' requested here
140 | return static_cast<flag_task*>(t.parent())->my_child_stolen;
| ^
14 warnings generated.
clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c number_of_alleles.cpp -o number_of_alleles.o
clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c profile.cpp -o profile.o
clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rare_prob.cpp -o rare_prob.o
clang++-21 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o DNAtools.so RcppExports.o class_DNTRare.o compare-utils.o compare.o compare_threaded.o number_of_alleles.o profile.o rare_prob.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5T6Fuq/R.INSTALL265f5b4e61ee/DNAtools/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5T6Fuq/R.INSTALL265f5b4e61ee/DNAtools/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5T6Fuq/R.INSTALL265f5b4e61ee/DNAtools/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-DNAtools/00new/DNAtools/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 (DNAtools)