I am trying to install Monocle3 (here) in Rstudio (R version 4.1.0) on M1 silicon MacOS Big Sur 11.4 using:
devtools::install_github('cole-trapnell-lab/leidenbase')
I get this error message, which makes it look like the cmath header is not working.
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
>
I have edited ~/.R/Makevars file using tricks here to "relink" SDK to the C++ compiler. Still not working.
I also tried updating Xcode, deleting and redownloading Xcode, and deleting and redownloading CommandLineTools.
Nothing is working.
Here is my current ~/.R/Makevars file:
CC=clang
CXX=clang++
CXXFLAGS= -O3 -pedantic -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
Thanks in advance for advice or workarounds.
