[Rcpp-devel] Cannot run rcpp due to missing include file(s)

Carl

First, thank you for this quick tip! I had no ~/.R directory and Makevars
didn’t exist when I searched

for it in Finder. So, I made the directdory ~/.R and then added a new file
“Makevars” to that directory.

I edited this file to add your PKG_CPPFLAGS:



(base) <hostname>-5:.R paul$ more Makevars


PKG_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include



Now I get another sequence of compiler errors. I’ll include only the first
several lines:



……….



In file included from fileb6e52d3a23c3.cpp:1:

In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:

In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:

In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:

In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:317:9:
error: no member named 'signbit' in the global namespace

using ::signbit;

      ~~^

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:318:9:
error: no member named 'fpclassify' in the global namespace

using ::fpclassify;

      ~~^

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:319:9:
error: no member named 'isfinite' in the global namespace; did you mean
'finite'?

using ::isfinite;

      ~~^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h:749:12:
note: 'finite' declared here

extern int finite(double)

           ^



*From: *Carl Ganz <carlganz at gmail.com>
*Date: *Sunday, May 3, 2020 at 11:02 AM
*To: *Paul Fishwick <metaphorz at gmail.com>
*Cc: *<rcpp-devel at lists.r-forge.r-project.org>
*Subject: *Re: [Rcpp-devel] Cannot run rcpp due to missing include file(s)



I experienced similar issues on Mac and was able to fix by adding
PKG_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include
to my .R/Makevars



My understanding is that Mac no longer uses the /usr/local/include so you
need to point it to the usr/include in the Developer SDK folder



On Sun, May 3, 2020 at 8:59 AM Paul Fishwick <metaphorz at gmail.com> wrote:




System: Mac OSX 11 (Catalina), Rstudio with R version 3.6.3 (but have also
tried 4.0 and 3.3),

Xcode version 11.4.1



Went to:  http://adv-r.had.co.nz/Rcpp.html#rcpp-intro



and tried library(rcpp) which worked fine because I previously had
installed the rcpp package.



The following yields an error in finding config.h. I did a "find" on
config.h and sure enough it is not

in the clang++ -I directory references. Here is what I have tried:



Installing Xcode's command line tools (which were installed using
xcode-select --install)

Also, downloaded and installed the version of clang8 and gfortran6.1 from:



https://cran.r-project.org/bin/macosx/tools/



The following error occurs when I try this rcpp example from Hadley but it
also happens whenever

I try to install an R package from source. The compile fails due to not
finding some include file.



I would have thought that installing clang8 would have also included the
proper include (.h) file directories

with their contents needed by R.



Is there something I am missing below? Thank you.

library(Rcpp)
cppFunction('int add(int x, int y, int z) {

+   int sum = x + y + z;
+   return sum;
+ }')
In file included from fileb6e52d3a23c3.cpp:1:
In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:304:
In file included from /usr/local/include/math.h:8:
In file included from /usr/local/include/features.h:10:
/usr/local/include/forwards.h:10:10: fatal error: 'config.h' file not found
#include "config.h"
         ^~~~~~~~~~
1 error generated.
make: *** [fileb6e52d3a23c3.o] Error 1
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
-DNDEBUG
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include"
-I"/private/var/folders/bt/1gd00p5s6n19m_bgh9b04gxc0000gp/T/RtmpRRyaky/sourceCpp-x86_64-apple-darwin15.6.0-1.0.4"
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include  -fPIC  -Wall -g -O2  -c fileb6e52d3a23c3.cpp -o
fileb6e52d3a23c3.o
Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir =
cacheDir,  :
  Error 1 occurred building shared library.