* installing *source* package ‘treehunt’ ...
** this is package ‘treehunt’ version ‘0.0.2’
** package ‘treehunt’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/treehunt/src'
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 genetic_algorithm.cpp -o genetic_algorithm.o
genetic_algorithm.cpp: In instantiation of ‘GeneticAlgorithm<TargetType>::GeneticAlgorithm(const PatientData<TargetType>&, const GAParams&, const Rcpp::Nullable<Rcpp::Vector<19> >&, const PWPScoreContext*) [with TargetType = int]’:
genetic_algorithm.cpp:367:16: required from here
367 | template class GeneticAlgorithm<int>;
| ^~~~~~~~~~~~~~~~~~~~~
genetic_algorithm.cpp:33:21: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
33 | if (seed.size() > params.population_size)
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
genetic_algorithm.cpp: In instantiation of ‘void GeneticAlgorithm<TargetType>::tournament_selection(std::vector<Solution>&) const [with TargetType = int]’:
genetic_algorithm.cpp:367:16: required from here
367 | template class GeneticAlgorithm<int>;
| ^~~~~~~~~~~~~~~~~~~~~
genetic_algorithm.cpp:171:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
171 | for (int j = 1; j < params_.tournament_size; ++j) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
genetic_algorithm.cpp: In instantiation of ‘GeneticAlgorithm<TargetType>::GeneticAlgorithm(const PatientData<TargetType>&, const GAParams&, const Rcpp::Nullable<Rcpp::Vector<19> >&, const PWPScoreContext*) [with TargetType = double]’:
genetic_algorithm.cpp:368:16: required from here
368 | template class GeneticAlgorithm<double>;
| ^~~~~~~~~~~~~~~~~~~~~~~~
genetic_algorithm.cpp:33:21: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
33 | if (seed.size() > params.population_size)
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
genetic_algorithm.cpp: In instantiation of ‘void GeneticAlgorithm<TargetType>::tournament_selection(std::vector<Solution>&) const [with TargetType = double]’:
genetic_algorithm.cpp:368:16: required from here
368 | template class GeneticAlgorithm<double>;
| ^~~~~~~~~~~~~~~~~~~~~~~~
genetic_algorithm.cpp:171:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
171 | for (int j = 1; j < params_.tournament_size; ++j) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from genetic_algorithm.h:6,
from genetic_algorithm.cpp:1:
score_functions.h: In instantiation of ‘static std::pair<ScoreFunctions<TargetType>::ScoreData, std::vector<double> > ScoreFunctions<TargetType>::compute_residuals_risk_with_stats(const PatientData<TargetType>&, const Solution&, bool) [with TargetType = int]’:
score_functions.h:938:45: required from ‘static double ScoreFunctions<TargetType>::compute_residuals_risk(const PatientData<TargetType>&, const Solution&, bool) [with TargetType = int]’
938 | return compute_residuals_risk_with_stats(data, solution).first.score;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
genetic_algorithm.cpp:88:62: required from ‘double GeneticAlgorithm<TargetType>::compute_score(const Solution&) const [with TargetType = int]’
88 | return ScoreFunctions<TargetType>::compute_residuals_risk(data_, sol);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
genetic_algorithm.cpp:367:16: required from here
367 | template class GeneticAlgorithm<int>;
| ^~~~~~~~~~~~~~~~~~~~~
score_functions.h:921:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
921 | if (K >= HL_values.size()) {
| ~~^~~~~~~~~~~~~~~~~~~
score_functions.h: In instantiation of ‘static std::pair<ScoreFunctions<TargetType>::ScoreData, std::vector<double> > ScoreFunctions<TargetType>::compute_residuals_risk_with_stats(const PatientData<TargetType>&, const Solution&, bool) [with TargetType = double]’:
score_functions.h:938:45: required from ‘static double ScoreFunctions<TargetType>::compute_residuals_risk(const PatientData<TargetType>&, const Solution&, bool) [with TargetType = double]’
938 | return compute_residuals_risk_with_stats(data, solution).first.score;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
genetic_algorithm.cpp:88:62: required from ‘double GeneticAlgorithm<TargetType>::compute_score(const Solution&) const [with TargetType = double]’
88 | return ScoreFunctions<TargetType>::compute_residuals_risk(data_, sol);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
genetic_algorithm.cpp:368:16: required from here
368 | template class GeneticAlgorithm<double>;
| ^~~~~~~~~~~~~~~~~~~~~~~~
score_functions.h:921:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
921 | if (K >= HL_values.size()) {
| ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 helpers.cpp -o helpers.o
helpers.cpp: In function ‘double normalized_distance(size_t, size_t, const std::vector<std::vector<int> >&, const std::vector<int>&, int)’:
helpers.cpp:13:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
13 | for(int k = begin_M_index_i; k < end_M_index_i; ++k )
| ~~^~~~~~~~~~~~~~~
helpers.cpp:18:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
18 | for(int k = begin_M_index_j; k < end_M_index_j; ++k)
| ~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 mcmc_algorithm.cpp -o mcmc_algorithm.o
mcmc_algorithm.cpp: In instantiation of ‘void MCMCAlgorithm<TargetType>::update_top_solutions(const Solution&, double, int) [with TargetType = int]’:
mcmc_algorithm.cpp:407:16: required from here
407 | template class MCMCAlgorithm<int>;
| ^~~~~~~~~~~~~~~~~~
mcmc_algorithm.cpp:208:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
208 | if (covered_patients > params_.beta) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
mcmc_algorithm.cpp: In instantiation of ‘void MCMCAlgorithm<TargetType>::update_top_solutions(const Solution&, double, int) [with TargetType = double]’:
mcmc_algorithm.cpp:408:16: required from here
408 | template class MCMCAlgorithm<double>;
| ^~~~~~~~~~~~~~~~~~~~~
mcmc_algorithm.cpp:208:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
208 | if (covered_patients > params_.beta) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from mcmc_algorithm.h:14,
from mcmc_algorithm.cpp:1:
score_functions.h: In instantiation of ‘static std::pair<ScoreFunctions<TargetType>::ScoreData, std::vector<double> > ScoreFunctions<TargetType>::compute_residuals_risk_with_stats(const PatientData<TargetType>&, const Solution&, bool) [with TargetType = int]’:
mcmc_algorithm.cpp:155:73: required from ‘typename ScoreFunctions<TargetType>::ScoreData MCMCAlgorithm<TargetType>::compute_score(const Solution&) const [with TargetType = int; typename ScoreFunctions<TargetType>::ScoreData = ScoreFunctions<int>::ScoreData]’
155 | return ScoreFunctions<TargetType>::compute_residuals_risk_with_stats(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
156 | data_, sol).first;
| ~~~~~~~~~~~
mcmc_algorithm.cpp:407:16: required from here
407 | template class MCMCAlgorithm<int>;
| ^~~~~~~~~~~~~~~~~~
score_functions.h:921:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
921 | if (K >= HL_values.size()) {
| ~~^~~~~~~~~~~~~~~~~~~
score_functions.h: In instantiation of ‘static std::pair<ScoreFunctions<TargetType>::ScoreData, std::vector<double> > ScoreFunctions<TargetType>::compute_residuals_risk_with_stats(const PatientData<TargetType>&, const Solution&, bool) [with TargetType = double]’:
mcmc_algorithm.cpp:155:73: required from ‘typename ScoreFunctions<TargetType>::ScoreData MCMCAlgorithm<TargetType>::compute_score(const Solution&) const [with TargetType = double; typename ScoreFunctions<TargetType>::ScoreData = ScoreFunctions<double>::ScoreData]’
155 | return ScoreFunctions<TargetType>::compute_residuals_risk_with_stats(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
156 | data_, sol).first;
| ~~~~~~~~~~~
mcmc_algorithm.cpp:408:16: required from here
408 | template class MCMCAlgorithm<double>;
| ^~~~~~~~~~~~~~~~~~~~~
score_functions.h:921:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
921 | if (K >= HL_values.size()) {
| ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 patient_data.cpp -o patient_data.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 patient_data_test.cpp -o patient_data_test.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 pwp_exports.cpp -o pwp_exports.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 pwp_score.cpp -o pwp_score.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 solution.cpp -o solution.o
solution.cpp: In static member function ‘static std::pair<Solution, Solution> Solution::crossover_single_point(const Solution&, const Solution&, const tree_structure&, std::mt19937&)’:
solution.cpp:235:11: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const __gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘const int’} [-Wsign-compare]
235 | if (i != upper_bound[i])
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 solution_test.cpp -o solution_test.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 tree_structure.cpp -o tree_structure.o
tree_structure.cpp: In member function ‘void tree_structure::initialize_upper_bound()’:
tree_structure.cpp:82:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
82 | for(size_t i = current_depth; i <= prev_dep; ++i){
| ~~^~~~~~~~~~~
tree_structure.cpp:86:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
86 | for(size_t i = 1; i < current_depth; ++i){
| ~~^~~~~~~~~~~~~~~
tree_structure.cpp: In member function ‘void tree_structure::add_names(const Rcpp::CharacterVector&)’:
tree_structure.cpp:96:19: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
96 | if(names.size() != depth_.size())
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 tree_test_exports.cpp -o tree_test_exports.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 treehunt.cpp -o treehunt.o
treehunt.cpp: In instantiation of ‘get_taker(Rcpp::List, Rcpp::DataFrame, SEXP, SEXP, SEXP, SEXP, Rcpp::DataFrame, SEXP, SEXP, SEXP)::<lambda(auto:1&)> [with auto:1 = PatientData<int>]’:
treehunt.cpp:1246:17: required from here
1246 | process_data(data);
| ~~~~~~~~~~~~^~~~~~
treehunt.cpp:1231:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1231 | for(int j = 0; j < data.size(); ++j){
| ~~^~~~~~~~~~~~~
treehunt.cpp: In instantiation of ‘get_taker(Rcpp::List, Rcpp::DataFrame, SEXP, SEXP, SEXP, SEXP, Rcpp::DataFrame, SEXP, SEXP, SEXP)::<lambda(auto:1&)> [with auto:1 = PatientData<double>]’:
treehunt.cpp:1249:17: required from here
1249 | process_data(data);
| ~~~~~~~~~~~~^~~~~~
treehunt.cpp:1231:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1231 | for(int j = 0; j < data.size(); ++j){
| ~~^~~~~~~~~~~~~
In file included from mcmc_algorithm.h:14,
from treehunt.cpp:2:
score_functions.h: In instantiation of ‘static std::pair<ScoreFunctions<TargetType>::ScoreData, std::vector<double> > ScoreFunctions<TargetType>::compute_residuals_risk_with_stats(const PatientData<TargetType>&, const Solution&, bool) [with TargetType = double]’:
treehunt.cpp:1117:78: required from here
1117 | score_data = ScoreFunctions<double>::compute_residuals_risk_with_stats(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
1118 | data, solution
| ~~~~~~~~~~~~~~
1119 | );
| ~
score_functions.h:921:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
921 | if (K >= HL_values.size()) {
| ~~^~~~~~~~~~~~~~~~~~~
score_functions.h: In instantiation of ‘static std::pair<ScoreFunctions<TargetType>::ScoreData, std::vector<double> > ScoreFunctions<TargetType>::compute_residuals_risk_bootstrap_with_stats(const PatientData<TargetType>&, const Solution&, bool) [with TargetType = double]’:
treehunt.cpp:1122:88: required from here
1122 | score_data = ScoreFunctions<double>::compute_residuals_risk_bootstrap_with_stats(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
1123 | data, solution
| ~~~~~~~~~~~~~~
1124 | );
| ~
score_functions.h:1027:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1027 | for (int i = 0; i < taker_vec.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o treehunt.so RcppExports.o genetic_algorithm.o helpers.o mcmc_algorithm.o patient_data.o patient_data_test.o pwp_exports.o pwp_score.o solution.o solution_test.o tree_structure.o tree_test_exports.o treehunt.o -fopenmp
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/treehunt/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/treehunt/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/treehunt/src'
installing to /data/localhost/ripley/R/packages/tests-devel/treehunt.Rcheck/00LOCK-treehunt/00new/treehunt/libs
** R
** 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 (treehunt)