* installing *source* package ‘gpboost’ ...
** this is package ‘gpboost’ version ‘1.6.5’
** 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) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
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
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,
from ./include/GPBoost/re_model.h:13,
from re_model.cpp:9:
./include/GPBoost/likelihoods.h: In instantiation of ‘void GPBoost::Likelihood<T_mat, T_chol>::CalcSecondDerivLogLikFirstDerivInformationAuxPar(const double*, const int*, const double*, int, double*, double*) const [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/likelihoods.h:5065:7: required from ‘void GPBoost::Likelihood<T_mat, T_chol>::CalcGradNegMargLikelihoodLaplaceApproxVecchia(const double*, const int*, const double*, std::map<int, Eigen::SparseMatrix<double> >&, std::map<int, Eigen::SparseMatrix<double> >&, std::map<int, std::vector<Eigen::SparseMatrix<double> > >&, std::map<int, std::vector<Eigen::SparseMatrix<double> > >&, bool, bool, bool, double*, GPBoost::vec_t&, double*, bool, int, bool, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&, GPBoost::den_mat_t, GPBoost::chol_den_mat_t, GPBoost::data_size_t, GPBoost::REModelTemplate<T_mat, T_chol>*, const std::vector<int>&) [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >; GPBoost::vec_t = Eigen::Matrix<double, -1, 1>; GPBoost::den_mat_t = Eigen::Matrix<double, -1, -1>; GPBoost::chol_den_mat_t = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>; GPBoost::data_size_t = int]’
5065 | CalcSecondDerivLogLikFirstDerivInformationAuxPar(y_data, y_data_int, location_par_ptr, ind_ap, second_deriv_loc_aux_par.data(), deriv_information_aux_par.data());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./include/GPBoost/re_model_template.h:1799:76: required from ‘void GPBoost::REModelTemplate<T_mat, T_chol>::CalcGradPars(const GPBoost::vec_t&, double, bool, bool, GPBoost::vec_t&, GPBoost::vec_t&, bool, bool, const double*, bool) [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >; GPBoost::vec_t = Eigen::Matrix<double, -1, 1>]’
1799 | likelihood_[cluster_i]->CalcGradNegMargLikelihoodLaplaceApproxVecchia(y_[cluster_i].data(), y_int_[cluster_i].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1800 | fixed_effects_cluster_i_ptr, B_[cluster_i], D_inv_[cluster_i], B_grad_[cluster_i], D_grad_[cluster_i],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1801 | calc_cov_aux_par_grad, calc_beta_grad, calc_grad_aux_par,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1802 | grad_cov_clus_i_ptr, grad_F_cluster_i,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1803 | grad_aux_clus_i_ptr, false, num_comps_total_, call_for_std_dev_coef, re_comps_ip_preconditioner_[cluster_i][0],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1804 | re_comps_cross_cov_preconditioner_[cluster_i][0], chol_ip_cross_cov_preconditioner_[cluster_i][0], chol_fact_sigma_ip_preconditioner_[cluster_i][0],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1805 | cluster_i, this, estimate_cov_par_index_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./include/GPBoost/re_model_template.h:1229:9: required from ‘void GPBoost::REModelTemplate<T_mat, T_chol>::OptimLinRegrCoefCovPar(const double*, const double*, int, double*, double*, int&, double*, double*, const double*, bool, bool, bool, bool, bool) [with T_mat = Eigen::SparseMatrix<double>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double>, 1, Eigen::AMDOrdering<int> >]’
1229 | CalcGradPars(cov_aux_pars, cov_aux_pars[0], false, true, unused_dummy, grad_beta, false, false, fixed_effects_ptr, false);
| ^~~~~~~~~~~~
re_model.cpp:348:40: required from here
348 | re_model_sp_->OptimLinRegrCoefCovPar(y_data,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
349 | nullptr,
| ~~~~~~~~
350 | 0,
| ~~
351 | cov_pars_.data(),
| ~~~~~~~~~~~~~~~~~
352 | nullptr,
| ~~~~~~~~
353 | num_it_,
| ~~~~~~~~
354 | cov_pars_.data(),
| ~~~~~~~~~~~~~~~~~
355 | nullptr,
| ~~~~~~~~
356 | fixed_effects,
| ~~~~~~~~~~~~~~
357 | true,
| ~~~~~
358 | called_in_GPBoost_algorithm,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
359 | reuse_learning_rates_from_previous_call,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 | false,
| ~~~~~~
361 | false);
| ~~~~~~
./include/GPBoost/likelihoods.h:11157:78: warning: unused variable ‘inv_t’ [-Wunused-variable]
11157 | const double inv_t = 1.0 / t;
| ^~~~~
./include/GPBoost/likelihoods.h: In instantiation of ‘void GPBoost::Likelihood<T_mat, T_chol>::CalcSecondDerivLogLikFirstDerivInformationAuxPar(const double*, const int*, const double*, int, double*, double*) const [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >]’:
./include/GPBoost/likelihoods.h:5065:7: required from ‘void GPBoost::Likelihood<T_mat, T_chol>::CalcGradNegMargLikelihoodLaplaceApproxVecchia(const double*, const int*, const double*, std::map<int, Eigen::SparseMatrix<double> >&, std::map<int, Eigen::SparseMatrix<double> >&, std::map<int, std::vector<Eigen::SparseMatrix<double> > >&, std::map<int, std::vector<Eigen::SparseMatrix<double> > >&, bool, bool, bool, double*, GPBoost::vec_t&, double*, bool, int, bool, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&, GPBoost::den_mat_t, GPBoost::chol_den_mat_t, GPBoost::data_size_t, GPBoost::REModelTemplate<T_mat, T_chol>*, const std::vector<int>&) [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >; GPBoost::vec_t = Eigen::Matrix<double, -1, 1>; GPBoost::den_mat_t = Eigen::Matrix<double, -1, -1>; GPBoost::chol_den_mat_t = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>; GPBoost::data_size_t = int]’
5065 | CalcSecondDerivLogLikFirstDerivInformationAuxPar(y_data, y_data_int, location_par_ptr, ind_ap, second_deriv_loc_aux_par.data(), deriv_information_aux_par.data());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./include/GPBoost/re_model_template.h:1799:76: required from ‘void GPBoost::REModelTemplate<T_mat, T_chol>::CalcGradPars(const GPBoost::vec_t&, double, bool, bool, GPBoost::vec_t&, GPBoost::vec_t&, bool, bool, const double*, bool) [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >; GPBoost::vec_t = Eigen::Matrix<double, -1, 1>]’
1799 | likelihood_[cluster_i]->CalcGradNegMargLikelihoodLaplaceApproxVecchia(y_[cluster_i].data(), y_int_[cluster_i].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1800 | fixed_effects_cluster_i_ptr, B_[cluster_i], D_inv_[cluster_i], B_grad_[cluster_i], D_grad_[cluster_i],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1801 | calc_cov_aux_par_grad, calc_beta_grad, calc_grad_aux_par,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1802 | grad_cov_clus_i_ptr, grad_F_cluster_i,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1803 | grad_aux_clus_i_ptr, false, num_comps_total_, call_for_std_dev_coef, re_comps_ip_preconditioner_[cluster_i][0],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1804 | re_comps_cross_cov_preconditioner_[cluster_i][0], chol_ip_cross_cov_preconditioner_[cluster_i][0], chol_fact_sigma_ip_preconditioner_[cluster_i][0],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1805 | cluster_i, this, estimate_cov_par_index_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./include/GPBoost/re_model_template.h:1229:9: required from ‘void GPBoost::REModelTemplate<T_mat, T_chol>::OptimLinRegrCoefCovPar(const double*, const double*, int, double*, double*, int&, double*, double*, const double*, bool, bool, bool, bool, bool) [with T_mat = Eigen::SparseMatrix<double, 1>; T_chol = Eigen::SimplicialLLT<Eigen::SparseMatrix<double, 1>, 1, Eigen::AMDOrdering<int> >]’
1229 | CalcGradPars(cov_aux_pars, cov_aux_pars[0], false, true, unused_dummy, grad_beta, false, false, fixed_effects_ptr, false);
| ^~~~~~~~~~~~
re_model.cpp:364:43: required from here
364 | re_model_sp_rm_->OptimLinRegrCoefCovPar(y_data,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
365 | nullptr,
| ~~~~~~~~
366 | 0,
| ~~
367 | cov_pars_.data(),
| ~~~~~~~~~~~~~~~~~
368 | nullptr,
| ~~~~~~~~
369 | num_it_,
| ~~~~~~~~
370 | cov_pars_.data(),
| ~~~~~~~~~~~~~~~~~
371 | nullptr,
| ~~~~~~~~
372 | fixed_effects,
| ~~~~~~~~~~~~~~
373 | true,
| ~~~~~
374 | called_in_GPBoost_algorithm,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
375 | reuse_learning_rates_from_previous_call,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
376 | false,
| ~~~~~~
377 | false);
| ~~~~~~
./include/GPBoost/likelihoods.h:11157:78: warning: unused variable ‘inv_t’ [-Wunused-variable]
11157 | const double inv_t = 1.0 / t;
| ^~~~~
./include/GPBoost/likelihoods.h: In instantiation of ‘void GPBoost::Likelihood<T_mat, T_chol>::CalcSecondDerivLogLikFirstDerivInformationAuxPar(const double*, const int*, const double*, int, double*, double*) const [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>]’:
./include/GPBoost/likelihoods.h:5065:7: required from ‘void GPBoost::Likelihood<T_mat, T_chol>::CalcGradNegMargLikelihoodLaplaceApproxVecchia(const double*, const int*, const double*, std::map<int, Eigen::SparseMatrix<double> >&, std::map<int, Eigen::SparseMatrix<double> >&, std::map<int, std::vector<Eigen::SparseMatrix<double> > >&, std::map<int, std::vector<Eigen::SparseMatrix<double> > >&, bool, bool, bool, double*, GPBoost::vec_t&, double*, bool, int, bool, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&, const std::vector<std::shared_ptr<GPBoost::RECompGP<Eigen::Matrix<double, -1, -1> > > >&, GPBoost::den_mat_t, GPBoost::chol_den_mat_t, GPBoost::data_size_t, GPBoost::REModelTemplate<T_mat, T_chol>*, const std::vector<int>&) [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>; GPBoost::vec_t = Eigen::Matrix<double, -1, 1>; GPBoost::den_mat_t = Eigen::Matrix<double, -1, -1>; GPBoost::chol_den_mat_t = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>; GPBoost::data_size_t = int]’
5065 | CalcSecondDerivLogLikFirstDerivInformationAuxPar(y_data, y_data_int, location_par_ptr, ind_ap, second_deriv_loc_aux_par.data(), deriv_information_aux_par.data());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./include/GPBoost/re_model_template.h:1799:76: required from ‘void GPBoost::REModelTemplate<T_mat, T_chol>::CalcGradPars(const GPBoost::vec_t&, double, bool, bool, GPBoost::vec_t&, GPBoost::vec_t&, bool, bool, const double*, bool) [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>; GPBoost::vec_t = Eigen::Matrix<double, -1, 1>]’
1799 | likelihood_[cluster_i]->CalcGradNegMargLikelihoodLaplaceApproxVecchia(y_[cluster_i].data(), y_int_[cluster_i].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1800 | fixed_effects_cluster_i_ptr, B_[cluster_i], D_inv_[cluster_i], B_grad_[cluster_i], D_grad_[cluster_i],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1801 | calc_cov_aux_par_grad, calc_beta_grad, calc_grad_aux_par,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1802 | grad_cov_clus_i_ptr, grad_F_cluster_i,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1803 | grad_aux_clus_i_ptr, false, num_comps_total_, call_for_std_dev_coef, re_comps_ip_preconditioner_[cluster_i][0],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1804 | re_comps_cross_cov_preconditioner_[cluster_i][0], chol_ip_cross_cov_preconditioner_[cluster_i][0], chol_fact_sigma_ip_preconditioner_[cluster_i][0],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1805 | cluster_i, this, estimate_cov_par_index_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./include/GPBoost/re_model_template.h:1229:9: required from ‘void GPBoost::REModelTemplate<T_mat, T_chol>::OptimLinRegrCoefCovPar(const double*, const double*, int, double*, double*, int&, double*, double*, const double*, bool, bool, bool, bool, bool) [with T_mat = Eigen::Matrix<double, -1, -1>; T_chol = Eigen::LLT<Eigen::Matrix<double, -1, -1>, 1>]’
1229 | CalcGradPars(cov_aux_pars, cov_aux_pars[0], false, true, unused_dummy, grad_beta, false, false, fixed_effects_ptr, false);
| ^~~~~~~~~~~~
re_model.cpp:380:41: required from here
380 | re_model_den_->OptimLinRegrCoefCovPar(y_data,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
381 | nullptr,
| ~~~~~~~~
382 | 0,
| ~~
383 | cov_pars_.data(),
| ~~~~~~~~~~~~~~~~~
384 | nullptr,
| ~~~~~~~~
385 | num_it_,
| ~~~~~~~~
386 | cov_pars_.data(),
| ~~~~~~~~~~~~~~~~~
387 | nullptr,
| ~~~~~~~~
388 | fixed_effects,
| ~~~~~~~~~~~~~~
389 | true,
| ~~~~~
390 | called_in_GPBoost_algorithm,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
391 | reuse_learning_rates_from_previous_call,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
392 | false,
| ~~~~~~
393 | false);
| ~~~~~~
./include/GPBoost/likelihoods.h:11157:78: warning: unused variable ‘inv_t’ [-Wunused-variable]
11157 | const double inv_t = 1.0 / t;
| ^~~~~
./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:7628:40: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized]
7628 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h:7628:43: warning: ‘p0’ may be used uninitialized [-Wmaybe-uninitialized]
7628 | double k, p0, q;
| ^~
./include/GPBoost/likelihoods.h:7634:9: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized]
7634 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:7628:47: note: ‘q’ was declared here
7628 | 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:7628:40: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized]
7628 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h:7628:43: warning: ‘p0’ may be used uninitialized [-Wmaybe-uninitialized]
7628 | double k, p0, q;
| ^~
./include/GPBoost/likelihoods.h:7634:9: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized]
7634 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:7628:47: note: ‘q’ was declared here
7628 | 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:7628:40: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized]
7628 | double k, p0, q;
| ^
./include/GPBoost/likelihoods.h:7628:43: warning: ‘p0’ may be used uninitialized [-Wmaybe-uninitialized]
7628 | double k, p0, q;
| ^~
./include/GPBoost/likelihoods.h:7634:9: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized]
7634 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:7628:47: note: ‘q’ was declared here
7628 | 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:6963:9: warning: ‘cross_cov_preconditioner’ may be used uninitialized [-Wmaybe-uninitialized]
6963 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:6949:50: note: ‘cross_cov_preconditioner’ was declared here
6949 | 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:6963:9: warning: ‘cross_cov_preconditioner’ may be used uninitialized [-Wmaybe-uninitialized]
6963 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:6949:50: note: ‘cross_cov_preconditioner’ was declared here
6949 | 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:6963:9: warning: ‘cross_cov_preconditioner’ may be used uninitialized [-Wmaybe-uninitialized]
6963 | #pragma omp parallel for schedule(static)
| ^~~
./include/GPBoost/likelihoods.h:6949:50: note: ‘cross_cov_preconditioner’ was declared here
6949 | 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)