* installing to library ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages’
* installing *source* package ‘GenomeAdmixR’ ...
** this is package ‘GenomeAdmixR’ version ‘2.1.12’
** package ‘GenomeAdmixR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpng03x4/R.INSTALL10a17245f378e7/GenomeAdmixR/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Fish.cpp -o Fish.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c helper_functions.cpp -o helper_functions.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:129:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Fish>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
129 | for (int i = 0; i < v.size(); ++i) {
| ~~^~~~~~~~~~
helper_functions.cpp: In function ‘double calculate_fitness(const Fish&, const std::vector<std::array<double, 5> >&, bool)’:
helper_functions.cpp:379:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::array<double, 5>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
379 | if (fitness_index > select[0].size()) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
helper_functions.cpp: In function ‘double calculate_fitness(const Fish_emp&, const std::vector<std::array<double, 5> >&, const std::vector<double>&, bool)’:
helper_functions.cpp:664:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
664 | if (focal_index < 0 || focal_index > focal.chromosome1.size()) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
helper_functions.cpp:672:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::array<double, 5>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
672 | if (fit_index > select[0].size()) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
helper_functions.cpp: In function ‘std::vector<std::array<double, 5> > convert_select_from_r(const Rcpp::NumericMatrix&)’:
helper_functions.cpp:996:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
996 | for (size_t i = 0; i < select.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~~
helper_functions.cpp:998:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
998 | for (size_t j = 0; j < select.ncol(); ++j) {
| ~~^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simulate.cpp -o simulate.o
simulate.cpp: In function ‘std::vector<Fish> simulate_Population(const std::vector<Fish>&, const Rcpp::NumericMatrix&, size_t, int, double, bool, arma::mat&, bool, const Rcpp::NumericVector&, bool, std::vector<double>&, bool, int, const std::vector<int>&, rnd_t&, int)’:
simulate.cpp:138:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
138 | for (size_t i = 0; i < select_r.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32,
from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24,
from util.h:15,
from simulate.cpp:21:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/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;
| ^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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*]’:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/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;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simulate_emp.cpp -o simulate_emp.o
simulate_emp.cpp: In function ‘Rcpp::List simulate_emp_cpp(const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, const Rcpp::NumericMatrix&, size_t, size_t, double, bool, bool, const Rcpp::NumericVector&, bool, double, const Rcpp::NumericMatrix&, int, const Rcpp::NumericVector&)’:
simulate_emp.cpp:267:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
267 | for (size_t i = 0; i < select.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~~
simulate_emp.cpp:269:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
269 | for (size_t j = 0; j < select.ncol(); ++j) {
| ~~^~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32,
from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24,
from util.h:15,
from simulate_emp.cpp:23:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/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;
| ^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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*]’:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/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;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simulate_migration.cpp -o simulate_migration.o
simulate_migration.cpp: In function ‘std::vector<std::vector<Fish> > simulate_two_populations(const std::vector<Fish>&, const std::vector<Fish>&, const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, int, double, bool, arma::mat&, bool, const Rcpp::NumericVector&, bool, std::vector<double>&, bool, int, const std::vector<int>&, double, int, rnd_t&)’:
simulate_migration.cpp:195:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
195 | for (size_t i = 0; i < select.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~~
simulate_migration.cpp:197:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
197 | for (size_t j = 0; j < select.ncol(); ++j) {
| ~~^~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32,
from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24,
from util.h:15,
from simulate_migration.cpp:22:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/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;
| ^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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*]’:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/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;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simulate_migration_emp.cpp -o simulate_migration_emp.o
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:412:25: 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]
412 | for (int j = 0; j < pop_size[1]; ++j) {
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32,
from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24,
from util.h:15,
from simulate_migration_emp.cpp:19:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/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;
| ^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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*]’:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/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;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o GenomeAdmixR.so Fish.o RcppExports.o helper_functions.o simulate.o simulate_emp.o simulate_migration.o simulate_migration_emp.o -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpng03x4/R.INSTALL10a17245f378e7/GenomeAdmixR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpng03x4/R.INSTALL10a17245f378e7/GenomeAdmixR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpng03x4/R.INSTALL10a17245f378e7/GenomeAdmixR/src'
installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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)