* installing *source* package ‘emcAdr’ ... ** this is package ‘emcAdr’ version ‘1.2’ ** package ‘emcAdr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-C++20/emcAdr/src' g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 DataManager.cpp -o DataManager.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 Individual.cpp -o Individual.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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.cpp -o MCMC.o DataManager.cpp: In function ‘std::vector > > ATCtoNumeric(const std::vector >&, const Rcpp::DataFrame&)’: DataManager.cpp:54:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 54 | while(posTree < cppTree.size() && token != cppTree[posTree]){ | ~~~~~~~~^~~~~~~~~~~~~~~~ DataManager.cpp:58:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 58 | if(posTree == cppTree.size()){ | ~~~~~~~~^~~~~~~~~~~~~~~~~ DataManager.cpp: In function ‘Rcpp::NumericVector histogramToDitribution(const std::vector >&)’: DataManager.cpp:95:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for(int i = 0 ; i < vec.size(); ++i){ | ~~^~~~~~~~~~~~ DataManager.cpp: In function ‘std::vector p_value_genetic_results(const std::vector >&, const Rcpp::List&, bool)’: DataManager.cpp:420:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 420 | for(int i = 0 ; i < cocktails.size(); ++i){ | ~~^~~~~~~~~~~~~~~~~~ DataManager.cpp:421:30: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 421 | if(cocktails[i].size() == k){ | ~~~~~~~~~~~~~~~~~~~~^~~~ DataManager.cpp: In function ‘std::vector p_value_cocktails(const std::vector >&, const std::vector > >&, const Rcpp::DataFrame&, const Rcpp::DataFrame&, int, bool)’: DataManager.cpp:486:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 486 | for(int i = 0 ; i < cocktails.size(); ++i){ | ~~^~~~~~~~~~~~~~~~~~ DataManager.cpp:487:29: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 487 | if(cocktails[i].size() == k){ | ~~~~~~~~~~~~~~~~~~~~^~~~ g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 Population.cpp -o Population.o Individual.cpp: In member function ‘bool Individual::matches(const std::vector >&, const std::vector >&) const’: Individual.cpp:26:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 26 | while (idx < observation.size() && !inIt){ | ~~~~^~~~~~~~~~~~~~~~~~~~ Individual.cpp:36:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 36 | if(idx == observation.size()) | ~~~~^~~~~~~~~~~~~~~~~~~~~ Individual.cpp: In member function ‘std::pair > Individual::computeRR(const std::vector > >&, const Rcpp::LogicalVector&, const std::vector >&, int, int) const’: Individual.cpp:57:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 57 | for(int i = 0; i < medications.size() ; ++i){ | ~~^~~~~~~~~~~~~~~~~~~~ Individual.cpp: In member function ‘std::pair > Individual::computePHypergeom(const std::vector > >&, const Rcpp::LogicalVector&, const std::vector >&, int, int, int, int) const’: Individual.cpp:111:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for(int i = 0; i < medications.size() ; ++i){ | ~~^~~~~~~~~~~~~~~~~~~~ Individual.cpp: In member function ‘bool Individual::isTrueCocktail(const std::vector >&) const’: Individual.cpp:186:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 186 | for(int i = 0; i < med.size() - 1 ; ++i){ | ~~^~~~~~~~~~~~~~~~ Individual.cpp: In member function ‘bool Individual::operator==(const Individual&) const’: Individual.cpp:203:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 203 | while(j < ind.medications_.size() && ind.medications_[j] != i){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ Individual.cpp:206:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 206 | if(j == ind.medications_.size()) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MCMC.cpp: In function ‘double addToBestCocktails(std::vector >&, const std::pair&, int, double, const std::vector >&)’: MCMC.cpp:42:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 42 | if(bestResults.size() < nbResults){ | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ MCMC.cpp: In function ‘Individual type1Mutation(const Individual&, int, double, bool)’: MCMC.cpp:270:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 270 | removeIndex = removeIndex == indiv.getMedications().size() ? removeIndex-1 : removeIndex; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MCMC.cpp: In function ‘Individual type2Mutation(const Individual&, int, const std::pair&)’: MCMC.cpp:328:36: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 328 | if(indiv.getMedications().size() == treeSize) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ MCMC.cpp: In function ‘std::pair >, std::vector > > treeDepthFather(const std::vector >&)’: MCMC.cpp:366:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 366 | for(int i = 0; i < ATC_length.size(); ++i){ | ~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 main.cpp -o main.o Individual.cpp: In member function ‘std::vector > Individual::getVertexList(const Rcpp::DataFrame&) const’: Individual.cpp:153:36: warning: ‘nextDepth’ may be used uninitialized [-Wmaybe-uninitialized] 153 | if(depth[idx] == nextDepth && (std::find(medications_.begin(),medications_.end(),idx) == medications_.end())){ Individual.cpp:137:20: note: ‘nextDepth’ was declared here 137 | int idx,depthMed,nextDepth,upperBMed; | ^~~~~~~~~ Population.cpp: In constructor ‘Population::Population(int, int, double, const std::vector >&)’: Population.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for(int i = 0 ; i < individuals.size(); ++i){ | ~~^~~~~~~~~~~~~~~~~~~~ Population.cpp: In member function ‘void Population::keepElite(int, Population&) const’: Population.cpp:64:21: warning: comparison of integer expressions of different signedness: ‘std::priority_queue, std::vector >, std::greater > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 64 | if (pq.size() < nbElite) { | ~~~~~~~~~~^~~~~~~~~ Population.cpp: In member function ‘void Population::crossover(int, const std::vector >&, const std::vector >&, const Rcpp::DataFrame&, double)’: Population.cpp:113:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 113 | for(int i = nbElite ; i < individuals_.size()-2; i+=2){ | ~~^~~~~~~~~~~~~~~~~~~~~~~ Population.cpp: In member function ‘void Population::mutate(int, double, const Rcpp::DataFrame&, const std::vector >&, double)’: Population.cpp:171:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 171 | for(int i = nbElite ; i < individuals_.size() ; ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~ Population.cpp: In member function ‘std::pair > >, std::vector > > Population::pretraitement(const std::vector >&, const std::vector >&) const’: Population.cpp:215:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 215 | for(int i = 0; i < individuals_.size(); ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~ Population.cpp: In member function ‘double Population::dist_norm(int, int, const IntMatrix&, const std::vector >&) const’: Population.cpp:249:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 249 | int max_idx_j = j == idx.size()-1 ? M.size() : idx[j+1]; | ~~^~~~~~~~~~~~~~~ Population.cpp: In member function ‘double Population::dist(int, int, const IntMatrix&, const std::vector >&) const’: Population.cpp:304:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | int max_idx_j = j == idx.size()-1 ? M.size() : idx[j+1]; | ~~^~~~~~~~~~~~~~~ Population.cpp: In member function ‘RealMatrix Population::similarity(const IntMatrix&, const std::vector >&) const’: Population.cpp:360:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 360 | for(int i = 0 ; i < idx.size()-1; ++i){ | ~~^~~~~~~~~~~~~~ Population.cpp:362:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 362 | for(int j = i+1; j < idx.size(); ++j){ | ~~^~~~~~~~~~~~ Population.cpp: In member function ‘RealMatrix Population::dissimilarity(const IntMatrix&, const std::vector >&, bool) const’: Population.cpp:383:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 383 | for(int i = 0; i < idx.size()-1; ++i){ | ~~^~~~~~~~~~~~~~ Population.cpp:385:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 385 | for(int j = i+1; j < idx.size(); ++j){ | ~~^~~~~~~~~~~~ Population.cpp: In member function ‘void Population::penalize(const std::vector >&, const std::vector >&)’: Population.cpp:411:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 411 | for(int i = 0 ; i < individuals_.size(); ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~ Population.cpp: In member function ‘int Population::bestIndividual() const’: Population.cpp:430:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 430 | for(int i = 1; i < individuals_.size() ; ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/numeric:64, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:68, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32, from Individual.h:10, from MCMC.h:5, from Population.h:4, from Population.cpp:1: /usr/include/c++/15/bits/stl_numeric.h: In instantiation of ‘constexpr _Tp std::accumulate(_InputIterator, _InputIterator, _Tp, _BinaryOperation) [with _InputIterator = __gnu_cxx::__normal_iterator*, vector > >; _Tp = double; _BinaryOperation = Population::getMean() const::&)>]’: Population.cpp:422:25: required from here 422 | return std::accumulate(individuals_.begin(), individuals_.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 423 | 0.0, [](double& a, const std::pair& b){ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | return a + b.first; | ~~~~~~~~~~~~~~~~~~~ 425 | }) / size; | ~~ /usr/include/c++/15/bits/stl_numeric.h:169:29: error: no match for call to ‘(Population::getMean() const::&)>) (std::remove_reference::type, const std::pair&)’ 169 | __init = __binary_op(_GLIBCXX_MOVE_IF_20(__init), *__first); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Population.cpp:423:32: note: there are 2 candidates 423 | 0.0, [](double& a, const std::pair& b){ | ^ /usr/include/c++/15/bits/stl_numeric.h:169:29: note: candidate 1: ‘double (*)(double&, const std::pair&)’ (conversion) 169 | __init = __binary_op(_GLIBCXX_MOVE_IF_20(__init), *__first); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/stl_numeric.h:169:29: note: conversion of argument 2 would be ill-formed: /usr/include/c++/15/bits/stl_numeric.h:169:29: error: cannot bind non-const lvalue reference of type ‘double&’ to an rvalue of type ‘std::remove_reference::type’ {aka ‘double’} Population.cpp:423:31: note: candidate 2: ‘Population::getMean() const::&)>’ (near match) 423 | 0.0, [](double& a, const std::pair& b){ | ^ Population.cpp:423:31: note: conversion of argument 1 would be ill-formed: Population.cpp:423:31: error: cannot bind non-const lvalue reference of type ‘double&’ to an rvalue of type ‘std::remove_reference::type’ {aka ‘double’} make[1]: *** [/data/gannet/ripley/R/cxx20/etc/Makeconf:201: Population.o] Error 1 main.cpp: In function ‘Rcpp::List DistributionApproximation(int, const Rcpp::DataFrame&, const Rcpp::DataFrame&, int, int, int, double, int, int, int, bool)’: main.cpp:212:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 212 | chosenVertexidx = chosenVertexidx == vertexX.size() ? vertexX.size()-1 : chosenVertexidx; | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ main.cpp: In function ‘std::vector MetricCalc_2(const std::vector >&, const std::vector >&, const std::vector >&, const std::vector > >&, const Rcpp::LogicalVector&, int, int)’: main.cpp:824:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 824 | for(int i = 0 ; i < observationsMedication.size(); ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp: In function ‘void print_list_in_file(const Rcpp::List&, const std::string&)’: main.cpp:1064:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1064 | for(int j = 0 ; j < mean_score_per_epoch.size() ; ++j){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Target 'all' not remade because of errors. make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-C++20/emcAdr/src' ERROR: compilation failed for package ‘emcAdr’ * removing ‘/data/gannet/ripley/R/packages/tests-C++20/emcAdr.Rcheck/emcAdr’