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

[Simon Urbanek]

On Mar 6, 2014, at 1:21 PM, Andy Jacobson <Andy.Jacobson at noaa.gov> wrote:

> 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.

https://stat.ethz.ch/pipermail/r-sig-mac/2014-January/010607.html

Admittedly a lot of the various posts on SIG-Mac have different keywords, because this is not  Maverick issue but rather Xcode 5 issue.


>  As far as updating R, I have the latest CRAN version...are you suggesting to go with a more recent build?
> 

Yes, either use the nightly build or R-3.0.3 binary (incidentally released today).

Cheers,
Simon


> 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
> 
> 
> 
> 
> 
>