* installing *source* package ‘malan’ ...
** package ‘malan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/malan/src'
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c PROTO.cpp -o PROTO.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_build_pedigrees.cpp -o api_build_pedigrees.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_igraph.cpp -o api_igraph.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_load_data.cpp -o api_load_data.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_simulate.cpp -o api_simulate.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_simulate_helper.cpp -o api_simulate_helper.o
api_igraph.cpp: In function 'Rcpp::XPtr<Population> from_igraph_rcpp(Rcpp::IntegerVector, Rcpp::IntegerMatrix)':
api_igraph.cpp:42:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
42 | for (size_t i = 0; i < edges.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~
api_load_data.cpp: In function 'void load_haplotypes(Rcpp::XPtr<Population>, Rcpp::IntegerVector, Rcpp::IntegerMatrix, bool)':
api_load_data.cpp:163:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
163 | for (int i = 0; i < N; ++i) {
| ~~^~~
api_simulate.cpp: In function 'Rcpp::List sample_geneology(size_t, int, int, int, bool, double, double, bool, bool)':
api_simulate.cpp:232:67: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
232 | while ((simulate_fixed_number_generations == true && generation < generations) || (simulate_fixed_number_generations == false && founders_left > 1)) {
| ~~~~~~~~~~~^~~~~~~~~~~~~
api_simulate.cpp:284:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
284 | if (generation <= extra_generations_full) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
api_simulate.cpp:346:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Rcpp::Vector<13> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
346 | for (int g = 0; g < individual_pids_tmp.size(); ++g) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_simulate_varying_size.cpp -o api_simulate_varying_size.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_autosomal.cpp -o api_utility_autosomal.o
api_simulate_varying_size.cpp: In function 'Rcpp::List sample_geneology_varying_size(Rcpp::IntegerVector, int, int, bool, double, double, bool)':
api_simulate_varying_size.cpp:147:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Rcpp::traits::storage_type<13>::type' {aka 'int'} [-Wsign-compare]
147 | for (size_t i = 0; i < population_sizes[generations-1]; ++i) {
api_simulate_varying_size.cpp:170:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Rcpp::traits::storage_type<13>::type' {aka 'int'} [-Wsign-compare]
170 | for (size_t i = 0; i < population_sizes[generations-1]; ++i) {
api_simulate_varying_size.cpp:178:42: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
178 | for (size_t generation = 1; generation < generations; ++generation) {
| ~~~~~~~~~~~^~~~~~~~~~~~~
api_simulate_varying_size.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 i = 0; i < population_size; ++i) {
| ~~^~~~~~~~~~~~~~~~~
api_simulate_varying_size.cpp:204:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
204 | for (size_t i = 0; i < children_population_size; ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
api_simulate_varying_size.cpp:227:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
227 | if (generation <= extra_generations_full) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
api_simulate_varying_size.cpp:228:42: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
228 | for (size_t father_i = 0; father_i < population_size; ++father_i) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~
api_simulate_varying_size.cpp:242:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
242 | for (size_t i = 0; i < population_size; ++i) {
| ~~^~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_autosomal_theta_unweighted.cpp -o api_utility_autosomal_theta_unweighted.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_autosomal_theta_weighted.cpp -o api_utility_autosomal_theta_weighted.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_haplotypes.cpp -o api_utility_haplotypes.o
api_utility_autosomal.cpp: In function 'void population_populate_autosomal_infinite_alleles(Rcpp::XPtr<Population>, double, bool)':
api_utility_autosomal.cpp:362:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
362 | for (int i = 1; i < alleles_support.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_individual.cpp -o api_utility_individual.o
api_utility_autosomal_theta_weighted.cpp: In function 'Rcpp::List estimate_autotheta_subpops_weighted_engine(std::vector<std::unordered_map<int, double> >, std::vector<std::unordered_map<int, double> >, std::vector<double>)':
api_utility_autosomal_theta_weighted.cpp:367:19: warning: comparison of integer expressions of different signedness: 'std::vector<std::unordered_map<int, double> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
367 | if (P_AA.size() != r) {
| ~~~~~~~~~~~~^~~~
api_utility_autosomal_theta_weighted.cpp:371:18: warning: comparison of integer expressions of different signedness: 'std::vector<std::unordered_map<int, double> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
371 | if (p_A.size() != r) {
| ~~~~~~~~~~~^~~~
api_utility_autosomal_theta_weighted.cpp:375:16: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
375 | if (n.size() != r) {
| ~~~~~~~~~^~~~
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_misc.cpp -o api_utility_misc.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_mixtures.cpp -o api_utility_mixtures.o
api_utility_haplotypes.cpp: In function 'void pedigrees_all_populate_haplotypes(Rcpp::XPtr<std::vector<Pedigree*> >, int, const Rcpp::NumericVector&, double, double, bool)':
api_utility_haplotypes.cpp:57:12: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
57 | if (loci != mut_rates.size()) {
| ~~~~~^~~~~~~~~~~~~~~~~~~
api_utility_haplotypes.cpp: In function 'void pedigrees_all_populate_haplotypes_ladder_bounded(Rcpp::XPtr<std::vector<Pedigree*> >, const Rcpp::NumericVector&, const Rcpp::IntegerVector&, const Rcpp::IntegerVector&, const Rcpp::Nullable<Rcpp::Function_Impl<Rcpp::PreserveStorage> >&, double, double, bool)':
api_utility_haplotypes.cpp:207:29: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
207 | if (mutation_rates.size() != lad_min.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
api_utility_haplotypes.cpp:211:29: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
211 | if (mutation_rates.size() != lad_max.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
api_utility_haplotypes.cpp: In function 'int count_haplotype_occurrences_individuals(Rcpp::List, Rcpp::IntegerVector)':
api_utility_haplotypes.cpp:433:23: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
433 | if (indv_h.size() != loci) {
| ~~~~~~~~~~~~~~^~~~~~~
api_utility_haplotypes.cpp: In function 'int count_haplotype_near_matches_individuals(Rcpp::List, Rcpp::IntegerVector, int)':
api_utility_haplotypes.cpp:480:23: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
480 | if (indv_h.size() != loci) {
| ~~~~~~~~~~~~~~^~~~~~~
api_utility_haplotypes.cpp: In function 'Rcpp::List haplotype_matches_individuals(Rcpp::List, Rcpp::IntegerVector)':
api_utility_haplotypes.cpp:532:23: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
532 | if (indv_h.size() != loci) {
| ~~~~~~~~~~~~~~^~~~~~~
api_utility_haplotypes.cpp: In function 'int count_haplotype_occurrences_pedigree(Rcpp::XPtr<Pedigree>, Rcpp::IntegerVector, int)':
api_utility_haplotypes.cpp:587:23: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
587 | if (dest_h.size() != loci) {
| ~~~~~~~~~~~~~~^~~~~~~
api_utility_haplotypes.cpp: In function 'Rcpp::IntegerMatrix pedigree_haplotype_near_matches_meiosis(Rcpp::XPtr<Individual>, int, int)':
api_utility_haplotypes.cpp:803:23: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
803 | if (dest_h.size() != loci) {
| ~~~~~~~~~~~~~~^~~~~~~
api_utility_haplotypes.cpp: In function 'Rcpp::IntegerVector haplotypes_to_hashes(Rcpp::XPtr<Population>, Rcpp::IntegerVector)':
api_utility_haplotypes.cpp:924:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
924 | for (size_t i = 0; i < n; ++i) {
| ~~^~~
api_utility_haplotypes.cpp:937:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
937 | for (int j = 0; j < indices.size(); ++j) {
| ~~^~~~~~~~~~~~~~~~
api_utility_haplotypes.cpp: In function 'Rcpp::List split_by_haplotypes(Rcpp::XPtr<Population>, Rcpp::IntegerVector)':
api_utility_haplotypes.cpp:965:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
965 | for (size_t i = 0; i < n; ++i) {
| ~~^~~
api_utility_haplotypes.cpp: In function 'Rcpp::List haplotype_partially_matches_individuals(Rcpp::List, Rcpp::IntegerVector, Rcpp::IntegerVector)':
api_utility_haplotypes.cpp:1043:23: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
1043 | if (indv_h.size() != loci) {
| ~~~~~~~~~~~~~~^~~~~~~
api_utility_haplotypes.cpp: In function 'Rcpp::XPtr<std::unordered_map<std::vector<int, std::allocator<int> >, std::vector<int, std::allocator<int> >*> > build_haplotype_hashmap(const Rcpp::List&, bool)':
api_utility_haplotypes.cpp:1096:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
1096 | for (size_t i = 0; i < n; ++i) {
| ~~^~~
api_utility_individual.cpp: In function 'int brothers_matching(Rcpp::XPtr<Individual>)':
api_utility_individual.cpp:329:23: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
329 | if (indv_h.size() != loci) {
| ~~~~~~~~~~~~~~^~~~~~~
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_mixtures_analyse.cpp -o api_utility_mixtures_analyse.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c api_utility_pedigree.cpp -o api_utility_pedigree.o
api_utility_mixtures_analyse.cpp: In function 'void analyse_set(int, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<int>&, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<std::unordered_set<int> >&, std::vector<std::vector<int> >&)':
api_utility_mixtures_analyse.cpp:43:68: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
43 | if ((haps_in_mixture_indices.size() + known_contributors.size()) != num_contributors) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp:53:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
53 | for (int set_i = 0; set_i < haps_in_mixture_indices.size(); set_i++) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp:72:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
72 | for (int set_i = 0; set_i < known_contributors.size(); ++set_i) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp:77:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
77 | for (int set_i = 0; set_i < suggested_contributors.size(); ++set_i) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp:100:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
100 | for (int level = 0; level < haps_in_mixture_indices.size(); level++) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp: In function 'void nested_loop_operation(std::vector<int>, std::vector<int>&, int, int, const std::vector<std::vector<int> >&, const std::vector<int>&, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<std::unordered_set<int> >&, std::vector<std::vector<int> >&)':
api_utility_mixtures_analyse.cpp:157:53: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
157 | if ((counters.size() + known_contributors.size()) != num_contributors) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp:161:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
161 | if (level == counters.size()) {
| ~~~~~~^~~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp:174:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
174 | for (int set_i = 1; set_i < counters.size(); set_i++) {
| ~~~~~~^~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp: In function 'Rcpp::List analyse_mixture_result(Rcpp::List&, const Rcpp::List&, const Rcpp::List&)':
api_utility_mixtures_analyse.cpp:251:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
251 | if (loci != true_donors[donor_i].size()) {
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp:274:24: warning: comparison of integer expressions of different signedness: 'std::unordered_set<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
274 | if (alleles.size() == K) {
| ~~~~~~~~~~~~~~~^~~~
api_utility_mixtures_analyse.cpp:359:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
359 | for (int term_i = 0; term_i < terms_Hd.size(); ++term_i) {
| ~~~~~~~^~~~~~~~~~~~~~~~~
api_utility_mixtures_analyse.cpp:390:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
390 | for (int term_i = 0; term_i < terms_Hp.size(); ++term_i) {
| ~~~~~~~^~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c class_Individual.cpp -o class_Individual.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c class_Pedigree.cpp -o class_Pedigree.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c class_Population.cpp -o class_Population.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c class_SimulateChooseFather.cpp -o class_SimulateChooseFather.o
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c helper_Individual.cpp -o helper_Individual.o
class_Individual.cpp: In member function 'void Individual::haplotype_mutate(const std::vector<double>&, double)':
class_Individual.cpp:380:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
380 | for (int loc = 0; loc < m_haplotype.size(); ++loc) {
| ~~~~^~~~~~~~~~~~~~~~~~~~
class_Individual.cpp: In member function 'void Individual::haplotype_mutate_ladder_bounded(const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, double)':
class_Individual.cpp:416:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
416 | for (int loc = 0; loc < m_haplotype.size(); ++loc) {
| ~~~~^~~~~~~~~~~~~~~~~~~~
class_Individual.cpp: In member function 'std::vector<Individual*> Individual::calculate_path_to(Individual*) const':
class_Individual.cpp:620:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Individual*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
620 | for (LCA_index = 0; LCA_index < path_this.size() && LCA_index < path_dest.size(); LCA_index++) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
class_Individual.cpp:620:65: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Individual*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
620 | for (LCA_index = 0; LCA_index < path_this.size() && LCA_index < path_dest.size(); LCA_index++) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c helper_generation.cpp -o helper_generation.o
class_SimulateChooseFather.cpp: In member function 'virtual int GammaVarianceRandomFather::get_father_i()':
class_SimulateChooseFather.cpp:68:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
68 | for (jj = 0; jj < population_size_1; ++jj) {
| ~~~^~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c test_misc.cpp -o test_misc.o
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o malan.so PROTO.o RcppExports.o api_build_pedigrees.o api_igraph.o api_load_data.o api_simulate.o api_simulate_helper.o api_simulate_varying_size.o api_utility_autosomal.o api_utility_autosomal_theta_unweighted.o api_utility_autosomal_theta_weighted.o api_utility_haplotypes.o api_utility_individual.o api_utility_misc.o api_utility_mixtures.o api_utility_mixtures_analyse.o api_utility_pedigree.o class_Individual.o class_Pedigree.o class_Population.o class_SimulateChooseFather.o helper_Individual.o helper_generation.o test_misc.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/malan/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/malan/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/malan/src'
installing to /data/gannet/ripley/R/packages/tests-devel/malan.Rcheck/00LOCK-malan/00new/malan/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (malan)