Trouble compiling packages under Mavericks
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
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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