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
