R devtool monocle3安装过程中出现MacOS Big Sur M1硅，cmath错误

Question

我正在尝试在M1硅MacOS Big Sur 11.4上的Rstudio (R版本4.1.0)中安装Monocle3 (here)，使用：

devtools::install_github('cole-trapnell-lab/leidenbase')

我得到了这个错误消息，这使它看起来像是cmath头不工作。

clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -I. -Icigraph/src -Icigraph/include -Icigraph/src/prpack -Ileidenalg/include -DUSING_R -DPRPACK_IGRAPH_SUPPORT -fPIC  -Wall -g -O2  -c cigraph/src/DensityGrid.cpp -o cigraph/src/DensityGrid.o
In file included from cigraph/src/DensityGrid.cpp:41:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:321:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:322:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:323:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
using ::isfinite;
      ~~^
/usr/local/include/math.h:752:12: note: 'finite' declared here
extern int finite(double)
           ^
In file included from cigraph/src/DensityGrid.cpp:41:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:324:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:325:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:326:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:327:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:738:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
In file included from cigraph/src/DensityGrid.cpp:41:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:328:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:767:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                            ^
In file included from cigraph/src/DensityGrid.cpp:41:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:329:9: error: no member named 'isless' in the global namespace
using ::isless;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:330:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:331:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:332:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:333:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
13 errors generated.
make: *** [cigraph/src/DensityGrid.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/leidenbase’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/37/6b_9y9v11nzftf912bbhbhr00000gn/T//Rtmph3567G/file159343f7bb5fc/leidenbase_0.1.3.tar.gz’ had non-zero exit status
> 

我已经编辑了~/.R/Makevars文件使用技巧here“重新链接”到C++编译器。还是不能工作。

我还尝试了更新Xcode，删除并重新下载Xcode，以及删除并重新下载CommandLineTools。

什么都不起作用。

这是我当前的~/.R/Makevars文件：

CC=clang
CXX=clang++
CXXFLAGS= -O3 -pedantic -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk

提前感谢您的建议或变通方法。

Answer 1

已通过以下方法解决此问题:将cmath文件中的#include<>更改为调用#include<\Full\path\here\to\math.h>，其中math.h与cmath位于同一目录中。