* installing *source* package ‘scistreer’ ...
** this is package ‘scistreer’ version ‘1.2.0’
** package ‘scistreer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.8’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/scistreer/src'
/usr/local/clang21/bin/clang++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -I"../inst/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -I"../inst/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c scistreer.cpp -o scistreer.o
In file included from scistreer.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/RcppParallel/include/RcppParallel.h:24:
In file included from /data/gannet/ripley/R/test-clang/RcppParallel/include/RcppParallel/TBB.h:11:
In file included from /data/gannet/ripley/R/test-clang/RcppParallel/include/tbb/concurrent_unordered_set.h:23:
In file included from /data/gannet/ripley/R/test-clang/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:37:
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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)
| ^
/data/gannet/ripley/R/test-clang/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;} \
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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;
| ^
/data/gannet/ripley/R/test-clang/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) {}
| ^
/data/gannet/ripley/R/test-clang/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){
| ^
/data/gannet/ripley/R/test-clang/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) )
| ^
/data/gannet/ripley/R/test-clang/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.
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
/usr/local/clang21/bin/clang++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o scistreer.so RcppExports.o scistreer.o -lpthread -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/scistreer/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/scistreer/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/scistreer/src'
installing to /data/gannet/ripley/R/packages/tests-clang/scistreer.Rcheck/00LOCK-scistreer/00new/scistreer/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (scistreer)