[ Started: 2023-03-31 11:41:55 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-devel/lib/R/library"     
trying URL 'https://cran.uni-muenster.de/src/contrib/xgboost_1.7.5.1.tar.gz'
Content type 'application/x-gzip' length 1080997 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘xgboost’ ...
** package ‘xgboost’ successfully unpacked and MD5 sums checked
** using staged installation
checking Backtrace lib... 
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking for backtrace in -lexecinfo... no
checking endian... 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
Makevars:17: -DXGBOOST_STRICT_R_MODE=1
Makevars:17: -DDMLC_LOG_BEFORE_THROW=0
Makevars:17: -DDMLC_ENABLE_STD_THREAD=1
Makevars:17: -DDMLC_DISABLE_STDIN=1
Makevars:17: -DDMLC_LOG_CUSTOMIZE=1
Makevars:17: -DXGBOOST_CUSTOMIZE_LOGGER=1
Makevars:17: -DRABIT_CUSTOMIZE_MSG_
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++17
Makevars:17: -DXGBOOST_STRICT_R_MODE=1
Makevars:17: -DDMLC_LOG_BEFORE_THROW=0
Makevars:17: -DDMLC_ENABLE_STD_THREAD=1
Makevars:17: -DDMLC_DISABLE_STDIN=1
Makevars:17: -DDMLC_LOG_CUSTOMIZE=1
Makevars:17: -DXGBOOST_CUSTOMIZE_LOGGER=1
Makevars:17: -DRABIT_CUSTOMIZE_MSG_
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c xgboost_R.cc -o xgboost_R.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c xgboost_custom.cc -o xgboost_custom.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/metric/metric.cc -o src/metric/metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/metric/elementwise_metric.cc -o src/metric/elementwise_metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/metric/multiclass_metric.cc -o src/metric/multiclass_metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/metric/rank_metric.cc -o src/metric/rank_metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/metric/auc.cc -o src/metric/auc.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/metric/survival_metric.cc -o src/metric/survival_metric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/objective/objective.cc -o src/objective/objective.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/objective/regression_obj.cc -o src/objective/regression_obj.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/objective/multiclass_obj.cc -o src/objective/multiclass_obj.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/objective/rank_obj.cc -o src/objective/rank_obj.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/objective/hinge.cc -o src/objective/hinge.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/objective/aft_obj.cc -o src/objective/aft_obj.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/objective/adaptive.cc -o src/objective/adaptive.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/gbm/gbm.cc -o src/gbm/gbm.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/gbm/gbtree.cc -o src/gbm/gbtree.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/gbm/gbtree_model.cc -o src/gbm/gbtree_model.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/gbm/gblinear.cc -o src/gbm/gblinear.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/gbm/gblinear_model.cc -o src/gbm/gblinear_model.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/simple_dmatrix.cc -o src/data/simple_dmatrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/data.cc -o src/data/data.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/sparse_page_raw_format.cc -o src/data/sparse_page_raw_format.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/ellpack_page.cc -o src/data/ellpack_page.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/gradient_index.cc -o src/data/gradient_index.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/gradient_index_page_source.cc -o src/data/gradient_index_page_source.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/gradient_index_format.cc -o src/data/gradient_index_format.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/sparse_page_dmatrix.cc -o src/data/sparse_page_dmatrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/proxy_dmatrix.cc -o src/data/proxy_dmatrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/data/iterative_dmatrix.cc -o src/data/iterative_dmatrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/predictor/predictor.cc -o src/predictor/predictor.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/predictor/cpu_predictor.cc -o src/predictor/cpu_predictor.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/constraints.cc -o src/tree/constraints.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/param.cc -o src/tree/param.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/tree_model.cc -o src/tree/tree_model.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/tree_updater.cc -o src/tree/tree_updater.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/updater_approx.cc -o src/tree/updater_approx.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/updater_colmaker.cc -o src/tree/updater_colmaker.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/updater_prune.cc -o src/tree/updater_prune.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/updater_quantile_hist.cc -o src/tree/updater_quantile_hist.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/updater_refresh.cc -o src/tree/updater_refresh.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/tree/updater_sync.cc -o src/tree/updater_sync.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/linear/linear_updater.cc -o src/linear/linear_updater.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/linear/updater_coordinate.cc -o src/linear/updater_coordinate.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/linear/updater_shotgun.cc -o src/linear/updater_shotgun.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/learner.cc -o src/learner.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/logging.cc -o src/logging.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/global_config.cc -o src/global_config.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/collective/communicator.cc -o src/collective/communicator.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/collective/socket.cc -o src/collective/socket.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/charconv.cc -o src/common/charconv.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/column_matrix.cc -o src/common/column_matrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/common.cc -o src/common/common.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/hist_util.cc -o src/common/hist_util.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/host_device_vector.cc -o src/common/host_device_vector.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/io.cc -o src/common/io.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/json.cc -o src/common/json.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/numeric.cc -o src/common/numeric.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/pseudo_huber.cc -o src/common/pseudo_huber.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/quantile.cc -o src/common/quantile.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/random.cc -o src/common/random.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/survival_util.cc -o src/common/survival_util.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/threading_utils.cc -o src/common/threading_utils.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/timer.cc -o src/common/timer.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/common/version.cc -o src/common/version.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/c_api/c_api.cc -o src/c_api/c_api.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c src/c_api/c_api_error.cc -o src/c_api/c_api_error.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c amalgamation/dmlc-minimum0.cc -o amalgamation/dmlc-minimum0.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c rabit/src/engine.cc -o rabit/src/engine.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c rabit/src/rabit_c_api.cc -o rabit/src/rabit_c_api.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/usr/local/include   -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic  -g -O2  -c rabit/src/allreduce_base.cc -o rabit/src/allreduce_base.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o xgboost.so ./xgboost_R.o ./xgboost_custom.o ./init.o ./src/metric/metric.o ./src/metric/elementwise_metric.o ./src/metric/multiclass_metric.o ./src/metric/rank_metric.o ./src/metric/auc.o ./src/metric/survival_metric.o ./src/objective/objective.o ./src/objective/regression_obj.o ./src/objective/multiclass_obj.o ./src/objective/rank_obj.o ./src/objective/hinge.o ./src/objective/aft_obj.o ./src/objective/adaptive.o ./src/gbm/gbm.o ./src/gbm/gbtree.o ./src/gbm/gbtree_model.o ./src/gbm/gblinear.o ./src/gbm/gblinear_model.o ./src/data/simple_dmatrix.o ./src/data/data.o ./src/data/sparse_page_raw_format.o ./src/data/ellpack_page.o ./src/data/gradient_index.o ./src/data/gradient_index_page_source.o ./src/data/gradient_index_format.o ./src/data/sparse_page_dmatrix.o ./src/data/proxy_dmatrix.o ./src/data/iterative_dmatrix.o ./src/predictor/predictor.o ./src/predictor/cpu_predictor.o ./src/tree/constraints.o ./src/tree/param.o ./src/tree/tree_model.o ./src/tree/tree_updater.o ./src/tree/updater_approx.o ./src/tree/updater_colmaker.o ./src/tree/updater_prune.o ./src/tree/updater_quantile_hist.o ./src/tree/updater_refresh.o ./src/tree/updater_sync.o ./src/linear/linear_updater.o ./src/linear/updater_coordinate.o ./src/linear/updater_shotgun.o ./src/learner.o ./src/logging.o ./src/global_config.o ./src/collective/communicator.o ./src/collective/socket.o ./src/common/charconv.o ./src/common/column_matrix.o ./src/common/common.o ./src/common/hist_util.o ./src/common/host_device_vector.o ./src/common/io.o ./src/common/json.o ./src/common/numeric.o ./src/common/pseudo_huber.o ./src/common/quantile.o ./src/common/random.o ./src/common/survival_util.o ./src/common/threading_utils.o ./src/common/timer.o ./src/common/version.o ./src/c_api/c_api.o ./src/c_api/c_api_error.o ./amalgamation/dmlc-minimum0.o ./rabit/src/engine.o ./rabit/src/rabit_c_api.o ./rabit/src/allreduce_base.o -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-xgboost/00new/xgboost/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (xgboost)

The downloaded source packages are in
	‘/tmp/RtmpViWvOn/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

[ Finished: 2023-03-31 11:47:42 CEST ]