Install log for 'GenomeAdmixR'

* installing *source* package ‘GenomeAdmixR’ ...
** package ‘GenomeAdmixR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++14
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/GenomeAdmixR/src'
g++-13 -std=gnu++14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 Fish.cpp -o Fish.o
g++-13 -std=gnu++14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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++-13 -std=gnu++14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 helper_functions.cpp -o helper_functions.o
g++-13 -std=gnu++14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 simulate.cpp -o simulate.o
g++-13 -std=gnu++14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 simulate_emp.cpp -o simulate_emp.o
g++-13 -std=gnu++14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 simulate_migration.cpp -o simulate_migration.o
g++-13 -std=gnu++14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 simulate_migration_emp.cpp -o simulate_migration_emp.o
helper_functions.cpp: In function 'arma::mat update_frequency_tibble(const std::vector<Fish>&, double, const std::vector<int>&, int, double)':
helper_functions.cpp:128:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Fish>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  128 |  for (int i = 0; i < v.size(); ++i) {
      |                  ~~^~~~~~~~~~
In file included from /usr/local/gcc13/include/c++/13.2.0/vector:62,
                 from helper_functions.h:11,
                 from helper_functions.cpp:8:
In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const double; _Up = double; bool _IsMove = false]',
    inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const double*; _OI = double*]' at /usr/local/gcc13/include/c++/13.2.0/bits/stl_algobase.h:506:30,
    inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const double*; _OI = double*]' at /usr/local/gcc13/include/c++/13.2.0/bits/stl_algobase.h:533:42,
    inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, vector<double> >; _OI = double*]' at /usr/local/gcc13/include/c++/13.2.0/bits/stl_algobase.h:540:31,
    inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const double*, vector<double> >; _OI = double*]' at /usr/local/gcc13/include/c++/13.2.0/bits/stl_algobase.h:633:7,
    inlined from 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]' at /usr/local/gcc13/include/c++/13.2.0/bits/stl_uninitialized.h:147:27,
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, vector<double> >; _ForwardIterator = double*]' at /usr/local/gcc13/include/c++/13.2.0/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, vector<double> >; _ForwardIterator = double*; _Tp = double]' at /usr/local/gcc13/include/c++/13.2.0/bits/stl_uninitialized.h:373:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/local/gcc13/include/c++/13.2.0/bits/stl_vector.h:603:31,
    inlined from 'std::vector<double> scale_markers(const std::vector<double>&, double)' at helper_functions.cpp:625:12:
/usr/local/gcc13/include/c++/13.2.0/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 8 is out of the bounds [0, 8] [-Warray-bounds=]
  437 |             __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
      |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
simulate_migration_emp.cpp: In function 'Rcpp::List simulate_migration_emp_cpp(const Rcpp::NumericMatrix&, const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, Rcpp::NumericMatrix, const Rcpp::NumericVector&, int, double, bool, bool, const Rcpp::NumericVector&, bool, double, double, const Rcpp::NumericMatrix&, int, const Rcpp::NumericVector&)':
simulate_migration_emp.cpp:425:25: warning: comparison of integer expressions of different signedness: 'int' and '__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} [-Wsign-compare]
  425 |       for (int j = 0; j < pop_size[1]; ++j) {
g++-13 -std=gnu++14 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o GenomeAdmixR.so Fish.o RcppExports.o helper_functions.o simulate.o simulate_emp.o simulate_migration.o simulate_migration_emp.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/GenomeAdmixR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/GenomeAdmixR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/GenomeAdmixR/src'
installing to /data/gannet/ripley/R/packages/tests-devel/GenomeAdmixR.Rcheck/00LOCK-GenomeAdmixR/00new/GenomeAdmixR/libs
** R
** data
** 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 (GenomeAdmixR)