由于共享库中的错误，自定义XGBoost安装失败

Question

我正在尝试从R中的https://github.com/robjhyndman/M4metalearning设置XGBoost的自定义版本。

当我运行devtools::install_github("pmontman/customxgboost")时，我得到这个错误：

> devtools::install_github("pmontman/customxgboost")
Downloading GitHub repo pmontman/customxgboost@master
✔  checking for file ‘/private/var/folders/5g/1cypnkxn3fs6tbk5ylfp1rqm0000gn/T/RtmpwXcO18/remotes1ff65ae3da8c/pmontman-customxgboost-ac8dacf/DESCRIPTION’ ...
─  preparing ‘xgboost’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
✔  checking vignette meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘xgboost_666.6.4.1.tar.gz’
   Warning: file 'xgboost/cleanup' did not have execute permissions: corrected

* installing *source* package ‘xgboost’ ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
/usr/local/bin/gcc-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/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=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c xgboost_R.cc -o xgboost_R.o
/usr/local/bin/gcc-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/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=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c xgboost_custom.cc -o xgboost_custom.o
/usr/local/bin/gcc-8 -I"/Library/Frameworks/R.framework/Resources/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=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/include   -fPIC  -Wall -g -O2  -c xgboost_assert.c -o xgboost_assert.o
/usr/local/bin/gcc-8 -I"/Library/Frameworks/R.framework/Resources/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=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
/usr/local/bin/gcc-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/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=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c amalgamation/xgboost-all0.cc -o amalgamation/xgboost-all0.o
/usr/local/bin/gcc-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/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=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c amalgamation/dmlc-minimum0.cc -o amalgamation/dmlc-minimum0.o
/usr/local/bin/gcc-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/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=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c rabit/src/engine_empty.cc -o rabit/src/engine_empty.o
/usr/local/bin/gcc-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/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=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c rabit/src/c_api.cc -o rabit/src/c_api.o
/usr/local/bin/gcc-8 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o xgboost.so ./xgboost_R.o ./xgboost_custom.o ./xgboost_assert.o ./init.o ./amalgamation/xgboost-all0.o ./amalgamation/dmlc-minimum0.o ./rabit/src/engine_empty.o ./rabit/src/c_api.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
Error: package or namespace load failed for ‘xgboost’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/xgboost/libs/xgboost.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/xgboost/libs/xgboost.so, 6): Symbol not found: __ZNSt11regex_errorD1Ev
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/xgboost/libs/xgboost.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.5/Resources/library/xgboost/libs/xgboost.so
Error: loading failed
Ejecución interrumpida
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/xgboost’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/xgboost’
Error in i.p(...) : 
  (convertido del aviso) installation of package ‘/var/folders/5g/1cypnkxn3fs6tbk5ylfp1rqm0000gn/T//RtmpwXcO18/file1ff67e4c38d5/xgboost_666.6.4.1.tar.gz’ had non-zero exit status

即时通信工具使用

我的~/.R/Makevars文件如下：

CC=/usr/local/bin/gcc-8
CXX=/usr/local/bin/g++-8
CXX11=/usr/local/bin/gcc-8

我还尝试按照以下指南安装原始的XGBoost：https://xgboost.readthedocs.io/en/latest/build.html

一切都很顺利。所以这个问题完全是R的问题，我有点卡住了。有什么建议吗？

Answer 1

最后我解决了这个问题，我将描述整个过程。

从本质上讲，你必须遵循以下步骤：

https://xgboost.readthedocs.io/en/latest/build.html

具体来说，这一点很重要：brew install gcc@8

此命令将支持openMP的gcc版本下载到XGBoost，这是一个重要的库，因为它具有一些并行特性。

可能是因为"symbol not found error“导致共享库xgboost.so失败。当您尝试链接从不同的gcc版本编译的对象时，就会出现这种情况。

更多信息请点击此处：What does "Symbol not found / Expected in: flat namespace" actually mean?

要解决此问题，我将~/.R/Makevars文件的内容更改为：

CC=/usr/local/bin/gcc-8 CXX=/usr/local/bin/g++-8 CXX11=/usr/local/bin/g++-8

注意: CX11与原始问题版本不同。

这解决了我的问题。

有关Makevars文件的更多信息，请访问：Understanding the contents of the Makevars file in R (macros, variables, ~/.R/Makevars and pkg/src/Makevars)

如果上述操作失败，建议删除R库并重新安装，可能是符号链接或类似链接有问题。

R库(Mac Os High Sierra)存储在以下位置：

/Library/Frameworks/R.framework/Versions/3.5/Resources/library/