* installing *source* package ‘jmotif’ ...
** this is package ‘jmotif’ version ‘1.3.0’
** package ‘jmotif’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/jmotif/src'
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/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
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c discord.cpp -o discord.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c distance.cpp -o distance.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c hot-sax.cpp -o hot-sax.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c jmotif.cpp -o jmotif.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c paa.cpp -o paa.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c repair.cpp -o repair.o
repair.cpp:119:7: warning: variable 'i' set but not used [-Wunused-but-set-variable]
119 | int i=0;
| ^
In file included from repair.cpp:1:
In file included from ../inst/include/jmotif.h:5:
In file included from /data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/vector:312:
In file included from /data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__vector/comparison.h:12:
In file included from /data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__algorithm/equal.h:22:
In file included from /data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__string/constexpr_c_functions.h:15:
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__memory/construct_at.h:67:5: warning: destructor called on non-final 'repair_symbol' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
67 | __loc->~_Tp();
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__memory/allocator_traits.h:313:10: note: in instantiation of function template specialization 'std::__destroy_at<repair_symbol>' requested here
313 | std::__destroy_at(__p);
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/deque:2417:21: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<repair_symbol>>::destroy<repair_symbol, 0>' requested here
2417 | __alloc_traits::destroy(__a, std::addressof(*__i));
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/deque:615:5: note: in instantiation of member function 'std::deque<repair_symbol>::clear' requested here
615 | clear();
| ^
../inst/include/jmotif.h:216:7: note: in instantiation of member function 'std::deque<repair_symbol>::~deque' requested here
216 | class repair_pool {
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__memory/construct_at.h:67:13: note: qualify call to silence this warning
67 | __loc->~_Tp();
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__memory/construct_at.h:67:5: warning: destructor called on non-final 'repair_guard' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
67 | __loc->~_Tp();
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__memory/allocator_traits.h:313:10: note: in instantiation of function template specialization 'std::__destroy_at<repair_guard>' requested here
313 | std::__destroy_at(__p);
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/deque:2417:21: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<repair_guard>>::destroy<repair_guard, 0>' requested here
2417 | __alloc_traits::destroy(__a, std::addressof(*__i));
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/deque:615:5: note: in instantiation of member function 'std::deque<repair_guard>::clear' requested here
615 | clear();
| ^
../inst/include/jmotif.h:216:7: note: in instantiation of member function 'std::deque<repair_guard>::~deque' requested here
216 | class repair_pool {
| ^
/data/gannet2/ripley/Sources/LLVM/LLVM-22.1.8-Linux-X64/bin/../include/c++/v1/__memory/construct_at.h:67:13: note: qualify call to silence this warning
67 | __loc->~_Tp();
| ^
3 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c repair_digram.cpp -o repair_digram.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c repair_guard.cpp -o repair_guard.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c repair_priority_queue.cpp -o repair_priority_queue.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c repair_rule.cpp -o repair_rule.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c repair_symbol.cpp -o repair_symbol.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c repair_symbol_record.cpp -o repair_symbol_record.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c rra.cpp -o rra.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c sax-vsm.cpp -o sax-vsm.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c sax.cpp -o sax.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c string.cpp -o string.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c utils.cpp -o utils.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c visit_registry.cpp -o visit_registry.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include/" -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c znorm.cpp -o znorm.o
clang++-22 -stdlib=libc++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o jmotif.so RcppExports.o discord.o distance.o hot-sax.o jmotif.o paa.o repair.o repair_digram.o repair_guard.o repair_priority_queue.o repair_rule.o repair_symbol.o repair_symbol_record.o rra.o sax-vsm.o sax.o string.o utils.o visit_registry.o znorm.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/jmotif/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/jmotif/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/jmotif/src'
installing to /data/gannet/ripley/R/packages/tests-clang/jmotif.Rcheck/00LOCK-jmotif/00new/jmotif/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (jmotif)