R , RCPP unsing MACOS ventura

I know that posting a makevars is somehow iffy, but I installed GCC with homebrew and my

~/.R/Makevars

Reads

CC=/opt/homebrew/bin/gcc-12 -fopenmp
CXX=/opt/homebrew/bin/g++-12 -fopenmp
CXX11=/opt/homebrew/bin/g++-12 -fopenmp
CXX14=/opt/homebrew/bin/g++-12 -fopenmp
CXX17=/opt/homebrew/bin/g++-12 -fopenmp
FLIBS=-L/opt/homebrew/opt/gfortran/lib
F77=/opt/homebrew/bin/gfortran
FC=/opt/R/arm64/gfortran/bin/gfortran -mtune=native
FLIBS=-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CPPFLAGS=-I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion

I installed the command line tools with

xcode-select --install

and I installed gcc with homebrew. It works:

library(Rcpp)
evalCpp( "1+1")

[1] 2


Federico Calboli
Tutkija
Genomiikka ja jalostus
Luonnonvarakeskus

From: R-SIG-Mac <r-sig-mac-bounces at r-project.org> on behalf of Michael Hall <mik3hall at gmail.com>
Date: Tuesday, 14. March 2023 at 13.52
To: r-sig-mac <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] R , RCPP unsing MACOS ventura

On Mar 14, 2023, at 6:00 AM, r-sig-mac-request at r-project.org wrote:

[R-SIG-Mac] R , RCPP unsing MACOS ventura

Google shows others have had the issue.

Suggestions include...

Uninstall and reinstall command line tools.

??

...following the wisdom of the "homebrew doctor" solves it, i.e. remove and reinstall:

sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select ?install

???


Rebuild with export SYSTEM_VERSION_COMPAT=1

Searched with?
<built-in>: error: unknown value ?13.2.0? of ?-mmacosx-version-min?





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On Mar 14, 2023, at 7:40 AM, Calboli Federico (LUKE) <federico.calboli at luke.fi> wrote:

I know that posting a makevars is somehow iffy, but I installed GCC with homebrew and my
 
~/.R/Makevars
 

It sounds like it is worth a try. However, I?m not sure it?s clear your OS and other versions match the original posters?

Did you build for the same issue?

It sounds like it is worth a try. However, I?m not sure it?s clear your OS and other versions match the original posters?

My bad, I?m on MacOS 13.2.1 arm64, with the latest XCode CLT

Did you build for the same issue?

I actually do not use Rcpp, I was just curious to know whether it works on my machine or not.  Apparently it does.



Federico Calboli
Tutkija
Genomiikka ja jalostus
Luonnonvarakeskus

If that is the case, can you actually post what the issue is? The original post had no details and did not follow up when asked for details. When googling the issue seems to arise in Homebrew, not the Apple tools so as I noted removing Homebrew should work.

Cheers,
Simon

On 15/03/2023, at 12:52 AM, Michael Hall <mik3hall at gmail.com> wrote:

On Mar 14, 2023, at 6:00 AM, r-sig-mac-request at r-project.org wrote:

[R-SIG-Mac] R , RCPP unsing MACOS ventura

Google shows others have had the issue.

Suggestions include...

Uninstall and reinstall command line tools.

??

...following the wisdom of the "homebrew doctor" solves it, i.e. remove and reinstall:

sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select ?install

???


Rebuild with export SYSTEM_VERSION_COMPAT=1 

Searched with?
<built-in>: error: unknown value ?13.2.0? of ?-mmacosx-version-min?




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On Mar 14, 2023, at 3:32 PM, Simon Urbanek <simon.urbanek at R-project.org> wrote:

If that is the case, can you actually post what the issue is? The original post had no details and did not follow up when asked for details. When googling the issue seems to arise in Homebrew, not the Apple tools so as I noted removing Homebrew should work.

Cheers,
Simon

On 15/03/2023, at 12:52 AM, Michael Hall <mik3hall at gmail.com> wrote:

On Mar 14, 2023, at 6:00 AM, r-sig-mac-request at r-project.org wrote:

[R-SIG-Mac] R , RCPP unsing MACOS ventura

Google shows others have had the issue.

Suggestions include...

Uninstall and reinstall command line tools.

??

...following the wisdom of the "homebrew doctor" solves it, i.e. remove and reinstall:

sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select ?install

???


Rebuild with export SYSTEM_VERSION_COMPAT=1 

Searched with?
<built-in>: error: unknown value ?13.2.0? of ?-mmacosx-version-min?

The general suggestion seemed to be for some reason to remove and reinstall the command line tools. The example I posted was one where it was the home-brew doctor that made that suggestion. Not that homebrew itself was the problem.

The

<built-in>: error: unknown value ?13.2.0? of ?-mmacosx-version-min?

Seemed to be what the underlying issue was? and was what I searched on

Well, what I saw in the searches what that it was a problem with Homebrew tools breaking on that flag. Again, it's all speculation, because no one posted the actual issue ... so it's anyone's guess what this is all about until someone actually posts the details I asked for - I don't see that problem myself, but I don't use Homebrew (at least not on the default PATH).

Cheers,
Simon

On 15/03/2023, at 9:45 AM, Michael Hall <mik3hall at gmail.com> wrote:

On Mar 14, 2023, at 3:32 PM, Simon Urbanek <simon.urbanek at R-project.org> wrote:

If that is the case, can you actually post what the issue is? The original post had no details and did not follow up when asked for details. When googling the issue seems to arise in Homebrew, not the Apple tools so as I noted removing Homebrew should work.

Cheers,
Simon

On 15/03/2023, at 12:52 AM, Michael Hall <mik3hall at gmail.com> wrote:

On Mar 14, 2023, at 6:00 AM, r-sig-mac-request at r-project.org wrote:

[R-SIG-Mac] R , RCPP unsing MACOS ventura

Google shows others have had the issue.

Suggestions include...

Uninstall and reinstall command line tools.

??

...following the wisdom of the "homebrew doctor" solves it, i.e. remove and reinstall:

sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select ?install

???


Rebuild with export SYSTEM_VERSION_COMPAT=1 

Searched with?
<built-in>: error: unknown value ?13.2.0? of ?-mmacosx-version-min?

The general suggestion seemed to be for some reason to remove and reinstall the command line tools. The example I posted was one where it was the home-brew doctor that made that suggestion. Not that homebrew itself was the problem.

The 

<built-in>: error: unknown value ?13.2.0? of ?-mmacosx-version-min?

Seemed to be what the underlying issue was? and was what I searched on

On Mar 14, 2023, at 3:50 PM, Simon Urbanek <simon.urbanek at R-project.org> wrote:

Well, what I saw in the searches what that it was a problem with Homebrew tools breaking on that flag. Again, it's all speculation, because no one posted the actual issue ... so it's anyone's guess what this is all about until someone actually posts the details I asked for - I don't see that problem myself, but I don't use Homebrew (at least not on the default PATH).

Cheers,
Simon

As you said earlier.

The error suggests your are using compilers that don't support your system.

It doesn?t seem to recognize a 13.2 system. This could well be because it is trying to use a homebrew gcc that isn?t playing well with the Xcode command line tools.

The xcode-select -version that I showed earlier was supposed to indicate what version of the command line tools you are using no matter with what Xcode.app although I?m not sure exactly how you are supposed to correspond the CLT version to the OS one.

gcc ?version should I think tell you if you have a homebrew or Apple one.

If homebrew is the culprit following the homebrew suggestion of uninstalling and reinstalling CLT would still seem to me to be worth the attempt.

If something is hardcoded in PATH messing up search orders that would be a different issue. 

Uninstalling homebrew as I think you suggested seems to be throwing out the baby, the bath water and the kitchen sink. There should be a less drastic solution.