[R-sig-ME] installing lme4.0 on OS X 10.9

[Levy, Roger]

Thanks so much, Tobias.  Unfortunately, setting up a Makevars file like you suggested simply leaves me with the same errors in R as I get in the command line:

> install.packages("lme4.0", repos="http://r-forge.r-project.org",type="source")
…
<snip>
…
clang -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o lme4.so init.o lmer.o local_stubs.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
…
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)


Any further thoughts or suggestions on this, anyone?

Best

Roger

On Feb 7, 2014, at 12:06 PM, Tobias Heed <tobias.heed.uhh at gmail.com> wrote:

> Dear Roger,
> 
> if I remember correctly, this solved the problem for me:
> on the top level of your user account, create a folder .R (if it’s not there yet);
> in there, create a new text file named Makevars;
> into this file, paste the following:
> 
> CC=clang
> CXX=clang++ -arch x86_64 -ftemplate-depth-256 -stdlib=libstdc++
> CXXFLAGS= -O3 -pedantic
> 
> hope it helps
> Best,
> Tobias
> 
> 
> From: Levy, Roger rlevy at ucsd.edu
> Reply: Levy, Roger rlevy at ucsd.edu
> Date: February 7,2014 at 20:59:11
> To: r-sig-mixed-models at r-project.org r-sig-mixed-models at r-project.org
> Subject:  [R-sig-ME] installing lme4.0 on OS X 10.9 
>> Hi all, 
>> 
>> My Mac laptop died and I am now reinstalling all my packages from scratch. Previously I was using lme4_0.999999-2 and I figure that with a fresh install, I might as well install lme4.0 instead. But I am having trouble compiling it: 
>> 
>> > install.packages("lme4.0", repos="http://r-forge.r-project.org",type="source") 
>> trying URL 'http://r-forge.r-project.org/src/contrib/lme4.0_0.999999-4.tar.gz' 
>> Content type 'application/x-gzip' length 772384 bytes (754 Kb) 
>> opened URL 
>> ================================================== 
>> downloaded 754 Kb 
>> 
>> * installing *source* package ‘lme4.0’ ... 
>> ** libs 
>> llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Matrix/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include" -fPIC -mtune=core2 -g -O2 -c init.c -o init.o 
>> /bin/sh: llvm-gcc-4.2: command not found 
>> 
>> 
>> This happens even after I install Xcode and also llvm-gcc42 on MacPorts; 
>> 
>> Does anyone have any suggestions? FWIW: 
>> 
>> > sessionInfo() 
>> R version 3.0.2 (2013-09-25) 
>> Platform: x86_64-apple-darwin10.8.0 (64-bit) 
>> 
>> locale: 
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 
>> 
>> attached base packages: 
>> [1] stats graphics grDevices utils datasets methods base 
>> 
>> loaded via a namespace (and not attached): 
>> [1] tools_3.0.2 
>> 
>> 
>> I’ve also tried installing from the command line; this bottoms out in a different error: 
>> 
>> $ R CMD build lme4.0 
>> … 
>> <snip> 
>> … 
>> ld: warning: directory not found for option ‘-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64’ 
>> ld: warning: directory not found for option ‘-L/usr/local/lib/x86_64’ 
>> ld: warning: directory not found for option ‘-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3’ 
>> ld: library not found for -lgfortran 
>> clang: error: linker command failed with exit code 1 (use -v to see invocation) 
>> make: *** [lme4.so] Error 1 
>> 
>> 
>> More generally, I’m having trouble figuring out what I should install in order to be able to compile lme4.0 from source. 
>> 
>> Best & many thanks in advance for any guidance, 
>> 
>> Roger Levy 
>> 
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