* installing *source* package ‘lightgbm’ ... ** package ‘lightgbm’ successfully unpacked and MD5 sums checked ** using staged installation checking location of R... /data/gannet/ripley/R/R-clang checking whether MM_PREFETCH works... yes checking whether MM_MALLOC works... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘clang version 18.1.4’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/lightgbm/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c boosting/boosting.cpp -o boosting/boosting.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c boosting/gbdt.cpp -o boosting/gbdt.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c boosting/gbdt_model_text.cpp -o boosting/gbdt_model_text.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c boosting/gbdt_prediction.cpp -o boosting/gbdt_prediction.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c boosting/prediction_early_stop.cpp -o boosting/prediction_early_stop.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c boosting/sample_strategy.cpp -o boosting/sample_strategy.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/bin.cpp -o io/bin.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/config.cpp -o io/config.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/config_auto.cpp -o io/config_auto.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/dataset.cpp -o io/dataset.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/dataset_loader.cpp -o io/dataset_loader.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/file_io.cpp -o io/file_io.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/json11.cpp -o io/json11.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/metadata.cpp -o io/metadata.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/parser.cpp -o io/parser.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/train_share_states.cpp -o io/train_share_states.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c io/tree.cpp -o io/tree.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c metric/dcg_calculator.cpp -o metric/dcg_calculator.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c metric/metric.cpp -o metric/metric.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c objective/objective_function.cpp -o objective/objective_function.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c network/linker_topo.cpp -o network/linker_topo.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c network/linkers_mpi.cpp -o network/linkers_mpi.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c network/linkers_socket.cpp -o network/linkers_socket.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c network/network.cpp -o network/network.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c treelearner/data_parallel_tree_learner.cpp -o treelearner/data_parallel_tree_learner.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c treelearner/feature_parallel_tree_learner.cpp -o treelearner/feature_parallel_tree_learner.o network/linkers_socket.cpp:174:7: warning: variable 'need_connect_cnt' set but not used [-Wunused-but-set-variable] 174 | int need_connect_cnt = 0; | ^ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c treelearner/gpu_tree_learner.cpp -o treelearner/gpu_tree_learner.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c treelearner/gradient_discretizer.cpp -o treelearner/gradient_discretizer.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c treelearner/linear_tree_learner.cpp -o treelearner/linear_tree_learner.o 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c treelearner/serial_tree_learner.cpp -o treelearner/serial_tree_learner.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c treelearner/tree_learner.cpp -o treelearner/tree_learner.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c treelearner/voting_parallel_tree_learner.cpp -o treelearner/voting_parallel_tree_learner.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c utils/openmp_wrapper.cpp -o utils/openmp_wrapper.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c c_api.cpp -o c_api.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./include -DEIGEN_MPL2_ONLY -DEIGEN_DONT_PARALLELIZE -DMM_PREFETCH=1 -DMM_MALLOC=1 -DUSE_SOCKET -DLGB_R_BUILD -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -pthread -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c lightgbm_R.cpp -o lightgbm_R.o /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o lightgbm.so boosting/boosting.o boosting/gbdt.o boosting/gbdt_model_text.o boosting/gbdt_prediction.o boosting/prediction_early_stop.o boosting/sample_strategy.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/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/gradient_discretizer.o treelearner/linear_tree_learner.o treelearner/serial_tree_learner.o treelearner/tree_learner.o treelearner/voting_parallel_tree_learner.o utils/openmp_wrapper.o c_api.o lightgbm_R.o -fopenmp -pthread make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/lightgbm/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/lightgbm/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/lightgbm/src' installing to /data/gannet/ripley/R/packages/tests-clang/lightgbm.Rcheck/00LOCK-lightgbm/00new/lightgbm/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (lightgbm)