[R-SIG-Mac] Strange C/C++ Compile Errors

[Wheeler, Matt (NIH/NIEHS) [E]]

I hope someone can help me with my C++/Rcpp compile issue. I am building a package, which will eventually be on CRAN, but I am currently looking to have it available to collaborators who use macOS. I have successfully compiled it for Linux and Windows (it passes the CRAN checks), but I have had no such luck for macOS. Here, I get strange compile errors based upon namespaces. For example, the first two errors are below:



In file included from RcppExports.cpp:4:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppGSL/include/RcppGSL.h:25:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppGSL/include/RcppGSLForward.h:24:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:66:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:

In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:308:

In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/math.h:308:

In file included from ./include/stdlib.h:36:

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:99:9: error: no member named 'size_t' in the global namespace

using ::size_t;



In file included from RcppExports.cpp:4:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppGSL/include/RcppGSL.h:25:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppGSL/include/RcppGSLForward.h:24:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:66:

In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:

In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:435:

In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:15:

In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:673:

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:319:5: error: no member named 'posix_memalign' in the global namespace

 ::posix_memalign(&__result, __alignment, __size);

 ~~^

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:330:5: error: reference to unresolved using declaration

 ::free(__ptr);



Essentially, all of the errors are based upon namespace issues.

I have seen that having a ~/.R/Makevars file messes things up, so I emptied that directory. I further have no h files in '/usr/local/include,'

which will cause other build errors (i.e. I use NLOPT and GSL), but I want to get through this right now. Based upon other threads, I have the following for Xcode:



%xcode-select -p

/Library/Developer/CommandLineTools

%xcrun --show-sdk-path

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

%which clang

/usr/bin/clang



Now, this is happening on two Macs. The first is an M1 with macOS Monterey 12.01, and I got it with a clean IT build. The second is the one I use for work. It is an Intel using Catalina 10.15.7 (19H1519). I can understand why the second one may be messed up. When the issue occurred almost a year ago, I was in a research phase, couldn't figure out the solution, installed brew gcc and had R compile with this 'nonstandard' compiler with many no-no hacks. It was a hack, but it worked. Now, I need to distribute this to the masses, and it is still not working on a fresh machine and a newer version of macOS. Before I go further, I want to see if there is some setup issue on my machine(s), possibly something I need to talk about to IT.



Further, the file RcppExports.cpp is automatically generated in Rcpp, so I don't think it is a code issue, but it is a dependency issue with clang, but here I am not knowledgeable enough to fix. Quite honestly, Apple�s compiler setup is baffling, but I am used to /usr/include/ etc.   I can also compile Rcpp from source code, and I have compiled other packages on these machines.



Thanks in advance,



Matt


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