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

[Prof Brian Ripley]

You have not shown us the compiler command line used, nor made a 
reproducible example available (and we might need both).

The suspicious line is

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

It looks like you may have a file in the package which is masking a 
system header, but we don't have any information to go on.


On 14/12/2021 13:06, Wheeler, Matt (NIH/NIEHS) [E] via R-SIG-Mac wrote:
> 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
> 
> 
> 	[[alternative HTML version deleted]]
> 
> 
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-- 
Brian D. Ripley,                  ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford