Rcpp broken by Mac OS Big Sur and Xcode 12.5

[gevro]

Rcpp gives many compilation errors on new MacOS Big Sur 11.3.1 and Xcode 12.5.

#~/Desktop/hello.cpp
#include <Rcpp.h>
// [[Rcpp::export]]
void hello()
{
  Rprintf("Hello, world!\n");
}

> library(Rcpp)
> sourceCpp("~/Desktop/hello.cpp")
In file included from hello.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/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 hello.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/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:327:9: error: no member named 'isgreater' in the global namespace
using ::isgreater;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:328:9: error: no member named 'isgreaterequal' in the global namespace
using ::isgreaterequal;
      ~~^
/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;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:339:9: error: no member named 'abs' in the global namespace; did you mean 'fabs'?
using ::abs;
      ~~^
/usr/local/include/math.h:417:15: note: 'fabs' declared here
extern double fabs(double);
              ^
In file included from hello.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:644:26: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:644:60: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                                                           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:645:18: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:645:50: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                                                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:650:17: error: no template named 'numeric_limits'
  static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix");
                ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [hello.o] Error 1
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include" -I"/Users/evrong01/Desktop" -I/usr/local/include   -fPIC  -Wall -g -O2  -c hello.cpp -o hello.o
Error in sourceCpp("~/Desktop/hello.cpp") : 
  Error 1 occurred building shared library.

Uninstalling and re-installing Xcode does not fix the problem. Every other possible way of installing and reinstalling xcode command line tools does not help.

[eddelbuettel]

@coatless @kevinushey and/or other macOS users: can you chime in?

We do have the pinned RcppArmadillo issue #268 at RcppCore/RcppArmadillo#268 but nothing for Rcpp. Maybe we need something to guide users in need who mistakenly think our code was a fault (and who cannot seem to even look at CRAN status results for Rcpp which beg to differ too...

[gevro]

Hi, Following the instructions on that post (though they're a little out of date) does not fix the problem. This issue occurred right after upgrading to Big Sur and Xcode 12.5. I suspect some issue in the automatic way these and/or xcode-command line tools are configured. I agree with your comment that it's not a bug in Rcpp, but I assume this issue is still relevant to Rcpp users who will likely experience this once they upgrade their OS.

[coatless]

Traveling at the moment. But, I can say that the macOS build is a okay with Rcpp. This is a local build issue.

[coatless]

You are using Xcode instead of the Xcode CLI based on the compilation statements. Are you sure you setup the CLI tools?

The path should be

'''sh

/Library/Developer/CommandLineTools
'''

not

/Applications/Xcode.app

Check path with

xcode-select --print-path

[gevro]

Hi, Yes I installed Xcode CLI:

$ xcode-select --install
xcode-select: error: command line tools are already installed, use "Software Update" to install updates

$ xcode-select -p
/Applications/Xcode.app/Contents/Developer

Is that not the correct configuration? That is the default configuration after uninstalling and re-installing Xcode 12.5 on Big Sur.

But I think I found the problem. Brew installed various files and symlinks in /usr/local/include. The /usr/local/include path was searched first during compilation and conflicted with other headers in the Xcode library paths. Deleting /usr/local/include and reinstalling Xcode and basic brew packages (but not brew packages for gcc and other compilers) seems to have fixed the problem.

So the problem was a conflict between brew and Xcode.

[eddelbuettel]

Closing this as it was a local setup issue. Thanks all.

[coatless]

For the future googler, it is ill-advised to use the homebrew (brew) build of R, e.g. brew install r, with binary versions of CRAN packages. Moreover, the compiler instructions are written for the official R build released by the CRAN team; not the brew build.

If using homebrew is a requirement, then a much better idea is to use the cask version of R, e.g. brew cask install r. The cask version "wraps" the official installer from CRAN's build machines instead of compiling R from the source.

---

First, note that you are using brew, not the official R binary. So, this is a "you break it; you own it" moment.

Secondly, regarding the problem on compilation tools used, the path issue would likely get picked up.
if you run:

brew doctor

Let's say homebrew isn't installed, but you were using Xcode.app for heavy macOS development instead of CommandLineTools. This can be picked programmatically up by typing in Terminal:

xcode-select --print-path

If the path is:

/Applications/Xcode.app

This indicates that the build toolchain is using Xcode-related suite of compilers. This needs to be switched to using the Xcode CLT. The switch is done in Terminal by typing:

sudo xcode-select -s /Library/Developer/CommandLineTools

[gevro]

Note also that in my case it was not a brew R installation that was the problem. I was using standard R. It was brew installation of other packages that put files in /usr/local/include that conflicted with Xcode. I don't know exactly which brew package it was, but it wasn't R, because I didn't have a brew R installation. It may have been gcc, or something like that.