* installing *source* package ‘LCMCR’ ... ** package ‘LCMCR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 13.0.1 20230419 (prerelease)’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-gcc13/LCMCR/src' /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c R_Interface/registration.cpp -o R_Interface/registration.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c R_Interface/R_Lcm_CR.cpp -o R_Interface/R_Lcm_CR.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c R_Interface/R_Lcm_CR_Strat.cpp -o R_Interface/R_Lcm_CR_Strat.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c NPLCM_CR_Basic_Freq.cpp -o NPLCM_CR_Basic_Freq.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c NPLCM_CR_Strat_Freq.cpp -o NPLCM_CR_Strat_Freq.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c daniel2/R_Environ_Simple.cpp -o daniel2/R_Environ_Simple.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c daniel2/CChain.cpp -o daniel2/CChain.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c daniel2/CParam.cpp -o daniel2/CParam.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c daniel2/CData.cpp -o daniel2/CData.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c daniel2/CParam_generic.cpp -o daniel2/CParam_generic.o /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c daniel2/CVariable_Container.cpp -o daniel2/CVariable_Container.o In file included from /usr/local/gcc13/include/c++/13.0.1/string:51, from daniel2/CData.h:28, from daniel2/Model_Environ.h:22, from daniel2/R_Environ_Simple.cpp:19: In static member function 'static void std::__copy_move::__assign_one(_Tp*, _Up*) [with _Tp = int; _Up = int]', inlined from 'static _Up* std::__copy_move_backward<_IsMove, true, std::random_access_iterator_tag>::__copy_move_b(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:751:20, inlined from '_BI2 std::__copy_move_backward_a2(_BI1, _BI1, _BI2) [with bool _IsMove = false; _BI1 = int*; _BI2 = int*]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:769:37, inlined from '_BI2 std::__copy_move_backward_a1(_BI1, _BI1, _BI2) [with bool _IsMove = false; _BI1 = int*; _BI2 = int*]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:778:51, inlined from '_OI std::__copy_move_backward_a(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = __gnu_cxx::__normal_iterator >]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:807:31, inlined from '_BI2 std::copy_backward(_BI1, _BI1, _BI2) [with _BI1 = int*; _BI2 = __gnu_cxx::__normal_iterator >]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:867:7, inlined from 'SEXPREC* R_Set_Param(SEXP, SEXP, SEXP)' at daniel2/R_Environ_Simple.cpp:276:20: /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:398:17: warning: array subscript -1 is outside array bounds of 'int [2147483647]' [-Warray-bounds=] 398 | { *__to = *__from; } | ~~~~~~^~~~~~~~~ In file included from /usr/local/gcc13/include/c++/13.0.1/x86_64-pc-linux-gnu/bits/c++allocator.h:33, from /usr/local/gcc13/include/c++/13.0.1/bits/allocator.h:46, from /usr/local/gcc13/include/c++/13.0.1/string:43: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/local/gcc13/include/c++/13.0.1/bits/alloc_traits.h:482:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:378:33, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:375:7, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:395:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:332:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:552:47, inlined from 'SEXPREC* R_Set_Param(SEXP, SEXP, SEXP)' at daniel2/R_Environ_Simple.cpp:275:32: /usr/local/gcc13/include/c++/13.0.1/bits/new_allocator.h:147:55: note: at offset -4 into object of size [4, 8589934588] allocated by 'operator new' 147 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In static member function 'static _Up* std::__copy_move_backward<_IsMove, true, std::random_access_iterator_tag>::__copy_move_b(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', inlined from '_BI2 std::__copy_move_backward_a2(_BI1, _BI1, _BI2) [with bool _IsMove = false; _BI1 = int*; _BI2 = int*]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:769:37, inlined from '_BI2 std::__copy_move_backward_a1(_BI1, _BI1, _BI2) [with bool _IsMove = false; _BI1 = int*; _BI2 = int*]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:778:51, inlined from '_OI std::__copy_move_backward_a(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = __gnu_cxx::__normal_iterator >]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:807:31, inlined from '_BI2 std::copy_backward(_BI1, _BI1, _BI2) [with _BI1 = int*; _BI2 = __gnu_cxx::__normal_iterator >]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:867:7, inlined from 'SEXPREC* R_Set_Param(SEXP, SEXP, SEXP)' at daniel2/R_Environ_Simple.cpp:276:20: /usr/local/gcc13/include/c++/13.0.1/bits/stl_algobase.h:748:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775807 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 748 | __builtin_memmove(__result - _Num, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/local/gcc13/include/c++/13.0.1/bits/alloc_traits.h:482:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:378:33, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:375:7, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:395:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:332:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/local/gcc13/include/c++/13.0.1/bits/stl_vector.h:552:47, inlined from 'SEXPREC* R_Set_Param(SEXP, SEXP, SEXP)' at daniel2/R_Environ_Simple.cpp:275:32: /usr/local/gcc13/include/c++/13.0.1/bits/new_allocator.h:147:55: note: at offset [-9223372036854775807, -5] into destination object of size [4, 8589934588] allocated by 'operator new' 147 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/local/gcc13/bin/g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-gcc13/include" -DNDEBUG -I. -DUSING_R -DHAVE_INLINE -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c daniel2/dan_array_utils.cpp -o daniel2/dan_array_utils.o /usr/local/gcc13/bin/g++ -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o LCMCR.so R_Interface/registration.o R_Interface/R_Lcm_CR.o R_Interface/R_Lcm_CR_Strat.o NPLCM_CR_Basic_Freq.o NPLCM_CR_Strat_Freq.o daniel2/R_Environ_Simple.o daniel2/CChain.o daniel2/CParam.o daniel2/CData.o daniel2/CParam_generic.o daniel2/CVariable_Container.o daniel2/dan_array_utils.o -lgsl -lgslcblas make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-gcc13/LCMCR/src' make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-gcc13/LCMCR/src' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-gcc13/LCMCR/src' installing to /data/gannet/ripley/R/packages/tests-gcc13/LCMCR.Rcheck/00LOCK-LCMCR/00new/LCMCR/libs ** R ** data ** 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 (LCMCR)