* installing *source* package ‘seqtrie’ ...
** package ‘seqtrie’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.0.1 20240503 (prerelease)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/seqtrie/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c CharCounter.cpp -o CharCounter.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RadixForest.cpp -o RadixForest.o
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:21,
from seqtrie_types.h:5,
from CharCounter.cpp:1:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RadixTree.cpp -o RadixTree.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:21,
from seqtrie_types.h:5,
from RadixForest.cpp:1:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:21,
from seqtrie_types.h:5,
from RadixTree.cpp:1:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:21,
from seqtrie_types.h:5,
from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c pairwise.cpp -o pairwise.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/numeric/ublas/traits.hpp:21,
from /data/gannet/ripley/R/test-dev/BH/include/boost/numeric/ublas/storage.hpp:27,
from /data/gannet/ripley/R/test-dev/BH/include/boost/numeric/ublas/vector.hpp:21,
from /data/gannet/ripley/R/test-dev/BH/include/boost/numeric/ublas/matrix.hpp:18,
from ../inst/include/seqtrie/pairwise.h:23,
from pairwise.cpp:2:
/data/gannet/ripley/R/test-dev/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
111 | public std::iterator<IC, T> {
| ^~~~~~~~
In file included from /usr/local/gcc14/include/c++/14.0.1/bits/stl_algobase.h:65,
from /usr/local/gcc14/include/c++/14.0.1/bits/specfun.h:43,
from /usr/local/gcc14/include/c++/14.0.1/cmath:3898,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/platform/compiler.h:100,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:62,
from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27,
from seqtrie_types.h:4,
from pairwise.cpp:1:
/usr/local/gcc14/include/c++/14.0.1/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
149 | public std::iterator<IC, T> {
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.0.1/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
204 | public std::iterator<IC, T> {
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.0.1/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:21,
from seqtrie_types.h:5:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o seqtrie.so CharCounter.o RadixForest.o RadixTree.o RcppExports.o pairwise.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/seqtrie/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/seqtrie/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/seqtrie/src'
installing to /data/gannet/ripley/R/packages/tests-devel/seqtrie.Rcheck/00LOCK-seqtrie/00new/seqtrie/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (seqtrie)