Install log for 'stringfish'

* installing *source* package ‘stringfish’ ...
** package ‘stringfish’ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
stringfish configure script
PCRE2 10.40 library detected -- skipping PCRE2 compilation
-lpcre2-8


configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-14 (GCC) 14.0.1 20240503 (prerelease)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/stringfish/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DRCPP_NO_RTTI -DPCRE2_CODE_UNIT_WIDTH=8 -DHAVE_CONFIG_H  -I.   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/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
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DRCPP_NO_RTTI -DPCRE2_CODE_UNIT_WIDTH=8 -DHAVE_CONFIG_H  -I.   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/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 sf_functions.cpp -o sf_functions.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 sf_functions.cpp:2:
/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;
      |            ^~~~~~~~~~~~~
/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::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::node*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:249:63:   required from 'tbb::interface5::internal::split_ordered_list<T, Allocator>::node* tbb::interface5::internal::split_ordered_list<T, Allocator>::node::atomic_set_next(tbb::interface5::internal::split_ordered_list<T, Allocator>::nodeptr_t, tbb::interface5::internal::split_ordered_list<T, Allocator>::nodeptr_t) [with T = std::pair<const RStringIndexer::rstring_info, std::atomic<int> >; Allocator = tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >; tbb::interface5::internal::split_ordered_list<T, Allocator>::nodeptr_t = tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::node*]'
  249 |             nodeptr_t exchange_node = tbb::internal::as_atomic(my_next).compare_and_swap(new_node, current_node);
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:510:41:   required from 'static tbb::interface5::internal::split_ordered_list<T, Allocator>::node* tbb::interface5::internal::split_ordered_list<T, Allocator>::try_insert_atomic(nodeptr_t, nodeptr_t, nodeptr_t) [with T = std::pair<const RStringIndexer::rstring_info, std::atomic<int> >; Allocator = tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >; nodeptr_t = tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::node*]'
  510 |         return previous->atomic_set_next(new_node, current_node);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:516:52:   required from 'std::pair<tbb::interface5::internal::solist_iterator<tbb::interface5::internal::split_ordered_list<T, Allocator>, typename std::allocator_traits<typename tbb::internal::allocator_rebind<A, T>::type>::value_type>, bool> tbb::interface5::internal::split_ordered_list<T, Allocator>::try_insert(raw_iterator, raw_iterator, nodeptr_t, size_type*) [with T = std::pair<const RStringIndexer::rstring_info, std::atomic<int> >; Allocator = tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >; typename std::allocator_traits<typename tbb::internal::allocator_rebind<A, T>::type>::value_type = std::pair<const RStringIndexer::rstring_info, std::atomic<int> >; typename tbb::internal::allocator_rebind<A, T>::type = std::allocator_traits<tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::rebind_alloc<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >; raw_iterator = tbb::interface5::internal::flist_iterator<tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >, std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >; nodeptr_t = tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::node*; size_type = long unsigned int]'
  516 |         nodeptr_t inserted_node = try_insert_atomic(it.get_node_ptr(), pnode, next.get_node_ptr());
      |                                   ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:1420:72:   required from 'std::pair<typename tbb::interface5::internal::split_ordered_list<typename Traits::value_type, typename Traits::allocator_type>::iterator, bool> tbb::interface5::internal::concurrent_unordered_base<Traits>::internal_insert(ValueType&&, nodeptr_t) [with AllowCreate = tbb::internal::bool_constant<false>; AllowDestroy = tbb::internal::bool_constant<true>; ValueType = std::pair<const RStringIndexer::rstring_info, std::atomic<int> >&; Traits = tbb::interface5::concurrent_unordered_map_traits<RStringIndexer::rstring_info, std::atomic<int>, tbb::interface5::internal::hash_compare<RStringIndexer::rstring_info, rstring_info_hash, std::equal_to<RStringIndexer::rstring_info> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >, false>; typename tbb::interface5::internal::split_ordered_list<typename Traits::value_type, typename Traits::allocator_type>::iterator = tbb::interface5::internal::solist_iterator<tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >, std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >; typename Traits::value_type = std::pair<const RStringIndexer::rstring_info, std::atomic<int> >; typename Traits::allocator_type = std::allocator_traits<tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::rebind_alloc<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >; nodeptr_t = tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::node*]'
 1420 |                 std::pair<iterator, bool> result = my_solist.try_insert(previous, where, pnode, &new_count);
      |                                                    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:1101:74:   required from 'std::pair<typename tbb::interface5::internal::split_ordered_list<typename Traits::value_type, typename Traits::allocator_type>::iterator, bool> tbb::interface5::internal::concurrent_unordered_base<Traits>::emplace(Args&& ...) [with Args = {RStringIndexer::rstring_info&, int&}; Traits = tbb::interface5::concurrent_unordered_map_traits<RStringIndexer::rstring_info, std::atomic<int>, tbb::interface5::internal::hash_compare<RStringIndexer::rstring_info, rstring_info_hash, std::equal_to<RStringIndexer::rstring_info> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >, false>; typename tbb::interface5::internal::split_ordered_list<typename Traits::value_type, typename Traits::allocator_type>::iterator = tbb::interface5::internal::solist_iterator<tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >, std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >; typename Traits::value_type = std::pair<const RStringIndexer::rstring_info, std::atomic<int> >; typename Traits::allocator_type = std::allocator_traits<tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::rebind_alloc<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > >]'
 1100 |         return internal_insert</*AllowCreate=*/tbb::internal::false_type,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
 1101 |                                /*AllowDestroy=*/tbb::internal::true_type>(pnode->my_element, pnode);
      |                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
sf_functions.cpp:1362:35:   required from here
 1362 |       auto p = table_hash->emplace(q, newval); // <iterator, bool>
      |                ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::node*' to 'tbb::atomic<tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::node*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::split_ordered_list<std::pair<const RStringIndexer::rstring_info, std::atomic<int> >, tbb::tbb_allocator<std::pair<const RStringIndexer::rstring_info, std::atomic<int> > > >::node]' [-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 -DRCPP_NO_RTTI -DPCRE2_CODE_UNIT_WIDTH=8 -DHAVE_CONFIG_H  -I.   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/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 PCRE2_wrapper/pcre2_wrapper.cpp -o PCRE2_wrapper/pcre2_wrapper.o
gcc-ar rcs libSFPCRE2.a  PCRE2_wrapper/pcre2_wrapper.o
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o stringfish.so RcppExports.o sf_functions.o -lpthread -L. -lSFPCRE2 -lpcre2-8
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/stringfish/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/stringfish/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/stringfish/src'
installing to /data/gannet/ripley/R/packages/tests-devel/stringfish.Rcheck/00LOCK-stringfish/00new/stringfish/libs
** R
** 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 (stringfish)