* installing *source* package ‘gpboost’ ...
** this is package ‘gpboost’ version ‘1.6.7’
** package ‘gpboost’ successfully unpacked and MD5 sums checked
** using staged installation
checking location of R... /data/gannet/ripley/R/R-devel
checking whether MM_PREFETCH works... yes
checking whether MM_MALLOC works... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
specified C++17
using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/gpboost/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 boosting/boosting.cpp -o boosting/boosting.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 boosting/gbdt.cpp -o boosting/gbdt.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 boosting/gbdt_model_text.cpp -o boosting/gbdt_model_text.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 boosting/gbdt_prediction.cpp -o boosting/gbdt_prediction.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 boosting/prediction_early_stop.cpp -o boosting/prediction_early_stop.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/bin.cpp -o io/bin.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/config.cpp -o io/config.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/config_auto.cpp -o io/config_auto.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/dataset.cpp -o io/dataset.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/dataset_loader.cpp -o io/dataset_loader.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/file_io.cpp -o io/file_io.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/json11.cpp -o io/json11.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/metadata.cpp -o io/metadata.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/parser.cpp -o io/parser.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/train_share_states.cpp -o io/train_share_states.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 io/tree.cpp -o io/tree.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 metric/dcg_calculator.cpp -o metric/dcg_calculator.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 metric/metric.cpp -o metric/metric.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 objective/objective_function.cpp -o objective/objective_function.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 network/ifaddrs_patch.cpp -o network/ifaddrs_patch.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 network/linker_topo.cpp -o network/linker_topo.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 network/linkers_mpi.cpp -o network/linkers_mpi.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 network/linkers_socket.cpp -o network/linkers_socket.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 network/network.cpp -o network/network.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 treelearner/data_parallel_tree_learner.cpp -o treelearner/data_parallel_tree_learner.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 treelearner/feature_parallel_tree_learner.cpp -o treelearner/feature_parallel_tree_learner.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 treelearner/gpu_tree_learner.cpp -o treelearner/gpu_tree_learner.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 treelearner/linear_tree_learner.cpp -o treelearner/linear_tree_learner.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 treelearner/serial_tree_learner.cpp -o treelearner/serial_tree_learner.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 treelearner/tree_learner.cpp -o treelearner/tree_learner.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 treelearner/voting_parallel_tree_learner.cpp -o treelearner/voting_parallel_tree_learner.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 c_api.cpp -o c_api.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 gpboost_R.cpp -o gpboost_R.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 re_model.cpp -o re_model.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 sparse_matrix_utils.cpp -o sparse_matrix_utils.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 GP_utils.cpp -o GP_utils.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 DF_utils.cpp -o DF_utils.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 Vecchia_utils.cpp -o Vecchia_utils.o
In file included from ./include/GPBoost/utils.h:17,
from ./include/GPBoost/cov_fcts.h:13,
from ./include/GPBoost/re_comp.h:13,
from ./include/GPBoost/re_model_template.h:15,
from ./include/GPBoost/re_model.h:13,
from re_model.cpp:9:
./include/GPBoost/re_model_template.h: In instantiation of ‘void GPBoost::REModelTemplate<T_mat, T_chol>::InitializeMatricesForUseWoodburyIdentity() [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/re_model_template.h:444:5: required from ‘GPBoost::REModelTemplate<T_mat, T_chol>::REModelTemplate(GPBoost::data_size_t, const GPBoost::data_size_t*, const char*, GPBoost::data_size_t, const double*, const GPBoost::data_size_t*, GPBoost::data_size_t, const int*, GPBoost::data_size_t, const double*, int, const double*, GPBoost::data_size_t, const char*, double, const char*, double, double, int, const char*, int, double, const char*, const char*, double, const char*, int, int, bool, bool, const double*, double) [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >; GPBoost::data_size_t = int]’
444 | InitializeMatricesForUseWoodburyIdentity();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
re_model.cpp:86:51: required from here
86 | has_weights, weights, likelihood_learning_rate));
| ^
./include/GPBoost/re_model_template.h:6843:132: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
6843 | CHECK((re_comps_vecchia_[cluster_i][0][0]->random_effects_indices_of_data_).size() == re_comps_vecchia_[cluster_i][0][0]->NumData());
./include/LightGBM/utils/log.h:41:9: note: in definition of macro ‘CHECK’
41 | if (!(condition)) \
| ^~~~~~~~~
./include/GPBoost/re_model_template.h: In instantiation of ‘void GPBoost::REModelTemplate<T_mat, T_chol>::DetermineCovarianceParameterIndicesNumCovPars() [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/re_model_template.h:454:4: required from ‘GPBoost::REModelTemplate<T_mat, T_chol>::REModelTemplate(GPBoost::data_size_t, const GPBoost::data_size_t*, const char*, GPBoost::data_size_t, const double*, const GPBoost::data_size_t*, GPBoost::data_size_t, const int*, GPBoost::data_size_t, const double*, int, const double*, GPBoost::data_size_t, const char*, double, const char*, double, double, int, const char*, int, double, const char*, const char*, double, const char*, int, int, bool, bool, const double*, double) [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >; GPBoost::data_size_t = int]’
454 | DetermineCovarianceParameterIndicesNumCovPars();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
re_model.cpp:86:51: required from here
86 | has_weights, weights, likelihood_learning_rate));
| ^
./include/GPBoost/re_model_template.h:6667:47: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘GPBoost::data_size_t’ {aka ‘int’} [-Wsign-compare]
6667 | CHECK(ind_par_.size() == num_comps_total_ + 1);
./include/LightGBM/utils/log.h:41:9: note: in definition of macro ‘CHECK’
41 | if (!(condition)) \
| ^~~~~~~~~
./include/GPBoost/re_model_template.h: In instantiation of ‘void GPBoost::REModelTemplate<T_mat, T_chol>::InitializeMatricesForUseWoodburyIdentity() [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/re_model_template.h:444:5: required from ‘GPBoost::REModelTemplate<T_mat, T_chol>::REModelTemplate(GPBoost::data_size_t, const GPBoost::data_size_t*, const char*, GPBoost::data_size_t, const double*, const GPBoost::data_size_t*, GPBoost::data_size_t, const int*, GPBoost::data_size_t, const double*, int, const double*, GPBoost::data_size_t, const char*, double, const char*, double, double, int, const char*, int, double, const char*, const char*, double, const char*, int, int, bool, bool, const double*, double) [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >; GPBoost::data_size_t = int]’
444 | InitializeMatricesForUseWoodburyIdentity();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
re_model.cpp:97:51: required from here
97 | has_weights, weights, likelihood_learning_rate));
| ^
./include/GPBoost/re_model_template.h:6843:132: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
6843 | CHECK((re_comps_vecchia_[cluster_i][0][0]->random_effects_indices_of_data_).size() == re_comps_vecchia_[cluster_i][0][0]->NumData());
./include/LightGBM/utils/log.h:41:9: note: in definition of macro ‘CHECK’
41 | if (!(condition)) \
| ^~~~~~~~~
./include/GPBoost/re_model_template.h: In instantiation of ‘void GPBoost::REModelTemplate<T_mat, T_chol>::DetermineCovarianceParameterIndicesNumCovPars() [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/re_model_template.h:454:4: required from ‘GPBoost::REModelTemplate<T_mat, T_chol>::REModelTemplate(GPBoost::data_size_t, const GPBoost::data_size_t*, const char*, GPBoost::data_size_t, const double*, const GPBoost::data_size_t*, GPBoost::data_size_t, const int*, GPBoost::data_size_t, const double*, int, const double*, GPBoost::data_size_t, const char*, double, const char*, double, double, int, const char*, int, double, const char*, const char*, double, const char*, int, int, bool, bool, const double*, double) [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >; GPBoost::data_size_t = int]’
454 | DetermineCovarianceParameterIndicesNumCovPars();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
re_model.cpp:97:51: required from here
97 | has_weights, weights, likelihood_learning_rate));
| ^
./include/GPBoost/re_model_template.h:6667:47: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘GPBoost::data_size_t’ {aka ‘int’} [-Wsign-compare]
6667 | CHECK(ind_par_.size() == num_comps_total_ + 1);
./include/LightGBM/utils/log.h:41:9: note: in definition of macro ‘CHECK’
41 | if (!(condition)) \
| ^~~~~~~~~
./include/GPBoost/re_model_template.h: In instantiation of ‘void GPBoost::REModelTemplate<T_mat, T_chol>::InitializeMatricesForUseWoodburyIdentity() [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>]’:
./include/GPBoost/re_model_template.h:444:5: required from ‘GPBoost::REModelTemplate<T_mat, T_chol>::REModelTemplate(GPBoost::data_size_t, const GPBoost::data_size_t*, const char*, GPBoost::data_size_t, const double*, const GPBoost::data_size_t*, GPBoost::data_size_t, const int*, GPBoost::data_size_t, const double*, int, const double*, GPBoost::data_size_t, const char*, double, const char*, double, double, int, const char*, int, double, const char*, const char*, double, const char*, int, int, bool, bool, const double*, double) [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>; GPBoost::data_size_t = int]’
444 | InitializeMatricesForUseWoodburyIdentity();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
re_model.cpp:108:51: required from here
108 | has_weights, weights, likelihood_learning_rate));
| ^
./include/GPBoost/re_model_template.h:6843:132: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
6843 | CHECK((re_comps_vecchia_[cluster_i][0][0]->random_effects_indices_of_data_).size() == re_comps_vecchia_[cluster_i][0][0]->NumData());
./include/LightGBM/utils/log.h:41:9: note: in definition of macro ‘CHECK’
41 | if (!(condition)) \
| ^~~~~~~~~
./include/GPBoost/re_model_template.h: In instantiation of ‘void GPBoost::REModelTemplate<T_mat, T_chol>::DetermineCovarianceParameterIndicesNumCovPars() [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>]’:
./include/GPBoost/re_model_template.h:454:4: required from ‘GPBoost::REModelTemplate<T_mat, T_chol>::REModelTemplate(GPBoost::data_size_t, const GPBoost::data_size_t*, const char*, GPBoost::data_size_t, const double*, const GPBoost::data_size_t*, GPBoost::data_size_t, const int*, GPBoost::data_size_t, const double*, int, const double*, GPBoost::data_size_t, const char*, double, const char*, double, double, int, const char*, int, double, const char*, const char*, double, const char*, int, int, bool, bool, const double*, double) [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>; GPBoost::data_size_t = int]’
454 | DetermineCovarianceParameterIndicesNumCovPars();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
re_model.cpp:108:51: required from here
108 | has_weights, weights, likelihood_learning_rate));
| ^
./include/GPBoost/re_model_template.h:6667:47: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘GPBoost::data_size_t’ {aka ‘int’} [-Wsign-compare]
6667 | CHECK(ind_par_.size() == num_comps_total_ + 1);
./include/LightGBM/utils/log.h:41:9: note: in definition of macro ‘CHECK’
41 | if (!(condition)) \
| ^~~~~~~~~
Vecchia_utils.cpp: In function ‘void GPBoost::find_nearest_neighbors_Vecchia_FSA_fast(const den_mat_t&, int, int, const den_mat_t&, const string_t&, std::vector<std::shared_ptr<RECompGP<Eigen::Matrix<double, -1, -1> > > >&, std::vector<std::vector<int> >&, std::vector<Eigen::Matrix<double, -1, -1> >&, std::vector<Eigen::Matrix<double, -1, -1> >&, int, int, bool&, bool, bool, bool, const int&, bool)’:
Vecchia_utils.cpp:462:37: warning: variable ‘start_dim’ set but not used [-Wunused-but-set-variable]
462 | int start_dim = 0;
| ^~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fopenmp -pthread -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 CG_utils.cpp -o CG_utils.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_spsolve.c -o cs_spsolve.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_reach.c -o cs_reach.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_dfs.c -o cs_dfs.o
In file included from ./include/GPBoost/re_model_template.h:19:
./include/GPBoost/likelihoods.h: In member function ‘void GPBoost::Likelihood<T_mat, T_chol>::PredictResponse(GPBoost::vec_t&, GPBoost::vec_t&, const GPBoost::vec_t&, const GPBoost::vec_t&, bool) [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/likelihoods.h:8437:40: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized]
8437 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h:8437:43: warning: ‘p0’ may be used uninitialized [-Wmaybe-uninitialized]
8437 | double k, p0, q;
| ^~
./include/GPBoost/likelihoods.h:8443:9: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized]
8443 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:8437:47: note: ‘q’ was declared here
8437 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h: In member function ‘void GPBoost::Likelihood<T_mat, T_chol>::PredictResponse(GPBoost::vec_t&, GPBoost::vec_t&, const GPBoost::vec_t&, const GPBoost::vec_t&, bool) [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/likelihoods.h:8437:40: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized]
8437 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h:8437:43: warning: ‘p0’ may be used uninitialized [-Wmaybe-uninitialized]
8437 | double k, p0, q;
| ^~
./include/GPBoost/likelihoods.h:8443:9: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized]
8443 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:8437:47: note: ‘q’ was declared here
8437 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h: In member function ‘void GPBoost::Likelihood<T_mat, T_chol>::PredictResponse(GPBoost::vec_t&, GPBoost::vec_t&, const GPBoost::vec_t&, const GPBoost::vec_t&, bool) [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>]’:
./include/GPBoost/likelihoods.h:8437:40: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized]
8437 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h:8437:43: warning: ‘p0’ may be used uninitialized [-Wmaybe-uninitialized]
8437 | double k, p0, q;
| ^~
./include/GPBoost/likelihoods.h:8443:9: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized]
8443 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:8437:47: note: ‘q’ was declared here
8437 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h: In member function ‘void GPBoost::Likelihood<T_mat, T_chol>::Sample_Posterior_LaplaceApprox_FSVA(const GPBoost::den_mat_t*, GPBoost::den_mat_t, GPBoost::den_mat_t, GPBoost::chol_den_mat_t, GPBoost::chol_den_mat_t, GPBoost::chol_den_mat_t, GPBoost::den_mat_t, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&) [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>]’:
./include/GPBoost/likelihoods.h:7771:9: warning: ‘cross_cov_preconditioner’ may be used uninitialized [-Wmaybe-uninitialized]
7771 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:7757:50: note: ‘cross_cov_preconditioner’ was declared here
7757 | const den_mat_t* cross_cov_preconditioner;
| ^~~~~~~~~~~~~~~~~~~~~~~~
./include/GPBoost/likelihoods.h: In member function ‘void GPBoost::Likelihood<T_mat, T_chol>::Sample_Posterior_LaplaceApprox_FSVA(const GPBoost::den_mat_t*, GPBoost::den_mat_t, GPBoost::den_mat_t, GPBoost::chol_den_mat_t, GPBoost::chol_den_mat_t, GPBoost::chol_den_mat_t, GPBoost::den_mat_t, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&) [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/likelihoods.h:7771:9: warning: ‘cross_cov_preconditioner’ may be used uninitialized [-Wmaybe-uninitialized]
7771 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:7757:50: note: ‘cross_cov_preconditioner’ was declared here
7757 | const den_mat_t* cross_cov_preconditioner;
| ^~~~~~~~~~~~~~~~~~~~~~~~
./include/GPBoost/likelihoods.h: In member function ‘void GPBoost::Likelihood<T_mat, T_chol>::Sample_Posterior_LaplaceApprox_FSVA(const GPBoost::den_mat_t*, GPBoost::den_mat_t, GPBoost::den_mat_t, GPBoost::chol_den_mat_t, GPBoost::chol_den_mat_t, GPBoost::chol_den_mat_t, GPBoost::den_mat_t, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&) [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/likelihoods.h:7771:9: warning: ‘cross_cov_preconditioner’ may be used uninitialized [-Wmaybe-uninitialized]
7771 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:7757:50: note: ‘cross_cov_preconditioner’ was declared here
7757 | const den_mat_t* cross_cov_preconditioner;
| ^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o gpboost.so boosting/boosting.o boosting/gbdt.o boosting/gbdt_model_text.o boosting/gbdt_prediction.o boosting/prediction_early_stop.o io/bin.o io/config.o io/config_auto.o io/dataset.o io/dataset_loader.o io/file_io.o io/json11.o io/metadata.o io/parser.o io/train_share_states.o io/tree.o metric/dcg_calculator.o metric/metric.o objective/objective_function.o network/ifaddrs_patch.o network/linker_topo.o network/linkers_mpi.o network/linkers_socket.o network/network.o treelearner/data_parallel_tree_learner.o treelearner/feature_parallel_tree_learner.o treelearner/gpu_tree_learner.o treelearner/linear_tree_learner.o treelearner/serial_tree_learner.o treelearner/tree_learner.o treelearner/voting_parallel_tree_learner.o c_api.o gpboost_R.o re_model.o sparse_matrix_utils.o GP_utils.o DF_utils.o Vecchia_utils.o CG_utils.o cs_spsolve.o cs_reach.o cs_dfs.o -fopenmp -pthread
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/gpboost/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/gpboost/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/gpboost/src'
installing to /data/gannet/ripley/R/packages/tests-devel/gpboost.Rcheck/00LOCK-gpboost/00new/gpboost/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (gpboost)