[R-SIG-Mac] Trouble compiling packages under Mavericks

[Andy Jacobson]

Simon,

Thanks for your reply.  I think this ought to be elevated to a FAQ, or mentioned in the R-admin Mavericks section, because I *still* can't find it in the R-Sig-Mac archives, even after you told me the information is there.  As far as updating R, I have the latest CRAN version...are you suggesting to go with a more recent build?

Thanks,

Andy

On Thu 06 Mar 2014, at 11:11 , Simon Urbanek <simon.urbanek at r-project.org> wrote:

> On Mar 6, 2014, at 1:03 PM, Andy Jacobson <andy.jacobson at noaa.gov> wrote:
> 
>> Howdy,
>> 
>> I experienced some hiccups trying to use R CMD INSTALL to compile/install packages, on Mavericks (OS X 10.9.2) with R-3.0.2 from CRAN.  I think I resolved them using a ~/.R/Makevars fix and I thought I'd report on that.
>> 
> 
> Please consider reading the archives before posting - this has been discussed do often that it should be almost a FAQ.
> This has been already addressed in recent R builds. The best advice is to update your R.
> 
> Cheers,
> Simon
> 
> 
>> The symptom I would get is complaints about "cc1" not understanding the "-arch" argument, as in:
>> 
>>>> R CMD INSTALL png_0.1-7.tar.gz 
>>> 
>>> * installing to library ‘/private/nfs/ct/lib/R-3.0/x86_64-apple-darwin10.8.0’
>>> * installing *source* package ‘png’ ...
>>> ** package ‘png’ successfully unpacked and MD5 sums checked
>>> ** libs
>>> llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    `libpng-config --cflags` -fPIC  -mtune=core2 -g -O2  -c read.c -o read.o
>>> cc1: error: unrecognized command line option "-arch"
>>> make: *** [read.o] Error 1
>>> ERROR: compilation failed for package ‘png’
>> 
>> llvm-gcc-4.2 is not the up-to-date XCode compiler.  That rather is "Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)".
>> 
>> Section C.3.4 ("Mavericks") of the R-admin guide suggests a "config.site" file with the following:
>> 
>> CC=clang
>> CXX=clang++
>> F77="gfortran-4.2 -arch x86_64"
>> FC=$F77
>> OBJC=clang
>> 
>> I put these definitions in my ~/.R/Makevars file and all packages compiled correctly after that.  I'm not sure this is correct.
>> 
>> Regards,
>> 
>> Andy
>> 
>> 
>> -- 
>> Andy Jacobson
>> andy.jacobson at noaa.gov
>> 
>> NOAA Earth System Research Lab
>> Global Monitoring Division
>> 325 Broadway R/GMD1
>> Boulder, Colorado 80305
>> 
>> 303/578-2237
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 

-- 
Andy Jacobson
andy.jacobson at noaa.gov

NOAA Earth System Research Lab
Global Monitoring Division
325 Broadway R/GMD1
Boulder, Colorado 80305

303/578-2237