It was a good suggestion. I went back to installing R 4.0 as you suggested. In
Rstudio, which I think
uses whatever R happens to be currently installed, I get into
a similar rcpp issue whenever I say “y” to compiling packages from source.
There seems
to be consistent disconnect of R finding certain files when compilation with
clang is required.
…………
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include
-I/usr/local/include -fPIC -Wall -g -O2 -c capture.c -o capture.o
In file included from capture.c:1:
In file included from
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:44:
In file included from
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:41:
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: *** [capture.o] Error 1
ERROR: compilation failed for package ‘rlang’
………………….
From: Carl Ganz <carlg...@gmail.com>
Date: Sunday, May 3, 2020 at 12:04 PM
To: Paul Fishwick <metaph...@gmail.com>
Cc: <rcpp-devel@lists.r-forge.r-project.org>
Subject: Re: [Rcpp-devel] Cannot run rcpp due to missing include file(s)
This is probably beyond my understanding at this point, but the solution I
offered worked for me with R 4.0 and it looks like this example is R 3.6
I vaguely remember some issues with interaction between older R version and
newer Xcode 11.4.1 so moving to R 4 might help
On Sun, May 3, 2020 at 9:25 AM Paul Fishwick <metaph...@gmail.com> wrote:
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 <carlg...@gmail.com>
Date: Sunday, May 3, 2020 at 11:02 AM
To: Paul Fishwick <metaph...@gmail.com>
Cc: <rcpp-devel@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 <metaph...@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.
>
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