* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘seqtrie’ ... ** package ‘seqtrie’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpH3NpDJ/R.INSTALL14e6f866fe9b09/seqtrie/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CharCounter.cpp -o CharCounter.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24, from seqtrie_types.h:5, from CharCounter.cpp:1: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RadixForest.cpp -o RadixForest.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24, from seqtrie_types.h:5, from RadixForest.cpp:1: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RadixTree.cpp -o RadixTree.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24, from seqtrie_types.h:5, from RadixTree.cpp:1: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24, from seqtrie_types.h:5, from RcppExports.cpp:4: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -DSEQTRIE_SMALL_ARRAY_SIZE=32 -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise.cpp -o pairwise.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/apply.hpp:24, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/serialization/array_optimization.hpp:18, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/serialization/array.hpp:26, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/matrix.hpp:18, from ../inst/include/seqtrie/pairwise.h:23, from pairwise.cpp:2: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ | - /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ | - In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/traits.hpp:21, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/storage.hpp:27: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 111 | public std::iterator { | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/platform/compiler.h:100, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/r/headers.h:66, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:30, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27, from seqtrie_types.h:4, from pairwise.cpp:1: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 149 | public std::iterator { | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 204 | public std::iterator { | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24, from seqtrie_types.h:5: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o seqtrie.so CharCounter.o RadixForest.o RadixTree.o RcppExports.o pairwise.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpH3NpDJ/R.INSTALL14e6f866fe9b09/seqtrie/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpH3NpDJ/R.INSTALL14e6f866fe9b09/seqtrie/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpH3NpDJ/R.INSTALL14e6f866fe9b09/seqtrie/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 converting help for package ‘seqtrie’ finding HTML links ... done RadixForest html RadixTree html covid_cdr3 html dist_matrix html dist_pairwise html dist_search html generate_cost_matrix html split_search html ** 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)