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

Mon Feb 10 19:08:29 CET 2014

Roger does not seem to have a working Fortran compiler which is required for lme4. He may want to install one, e.g. from
http://cran.r-project.org/bin/macosx/tools/

BTW: please don't point people to obsolete SO posts - the proper cure to most Mavericks problems is to simply install more recent build of R.

Cheers,
Simon

On Feb 10, 2014, at 6:09 AM, Cole, Tim <tim.cole at ucl.ac.uk> wrote:

> I'm forwarding this to R-sig-Mac.
> 
> Tim Cole
> --
> Tim.Cole at ucl.ac.uk<mailto:Tim.Cole at ich.ucl.ac.uk> Phone +44(0)20 7905 2666 Fax +44(0)20 7905 2381
> Centre for Paediatric Epidemiology and Biostatistics
> UCL Institute of Child Health, London WC1N 1EH, UK
> 
> From: Tobias Heed <tobias.heed.uhh at gmail.com<mailto:tobias.heed.uhh at gmail.com>>
> To: Levy, Roger <rlevy at ucsd.edu<mailto:rlevy at ucsd.edu>>
> Cc: "=?utf-8?Q?r-sig-mixed-models=40r-project.org?="
> <r-sig-mixed-models at r-project.org<mailto:r-sig-mixed-models at r-project.org>>
> Subject: Re: [R-sig-ME] installing lme4.0 on OS X 10.9
> Message-ID: <etPan.52f88faa.3730bb65.2e5a at Macintosh.local<mailto:etPan.52f88faa.3730bb65.2e5a at Macintosh.local>>
> Content-Type: text/plain
> 
> Roger,
> 
> sorry to hear this didn’t work. Unfortunately, I do not recall everything I tried back then. I do recall that the problem was that gcc doesn’t come with Mavericks. A few things still,
> 1, after reinstalling your Mac, did you update XCode? This is probably necessary.
> 2, after making the Makevars file, did you restart R?
> 
> Assuming that most probably you did both, I found these links in my notes, maybe they can point you in the right direction.
> http://stackoverflow.com/questions/19503995/error-when-with-xcode-5-0-and-rcpp-command-line-tools-are-installed
> http://stackoverflow.com/questions/19533220/cannot-install-r-package-from-source-in-mac-osx-maverick
> 
> hope this helps.
> Best,
> Tobias
> 
> 
> --
> --------------------------------------------------------------------------------------------------------------
> Tobias Heed, PhD
> Biological Psychology and Neuropsychology
> Department of Psychology & Human Movement Science  |  University of Hamburg
> Von-Melle-Park 11, Room 208  |  D-20146 Hamburg, Germany
> Phone: (49) 40 - 42838 5831  |  Fax:   (49) 40 - 42838 6591
> tobias.heed at uni-hamburg.de<mailto:tobias.heed at uni-hamburg.de>  |  Website  |  Google Scholar
> --------------------------------------------------------------------------------------------------------------
> From: Levy, Roger rlevy at ucsd.edu<mailto:rlevy at ucsd.edu>
> Reply: Levy, Roger rlevy at ucsd.edu<mailto:rlevy at ucsd.edu>
> Date: February 9,2014 at 23:41:48
> To: Tobias Heed tobias.heed.uhh at gmail.com<mailto:tobias.heed.uhh at gmail.com>
> Cc: r-sig-mixed-models at r-project.org<mailto:r-sig-mixed-models at r-project.org> r-sig-mixed-models at r-project.org<mailto:r-sig-mixed-models at r-project.org>
> Subject:  Re: [R-sig-ME] installing lme4.0 on OS X 10.9
> 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<mailto: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<mailto:rlevy at ucsd.edu>
> Reply: Levy, Roger rlevy at ucsd.edu<mailto:rlevy at ucsd.edu>
> Date: February 7,2014 at 20:59:11
> To: r-sig-mixed-models at r-project.org<mailto:r-sig-mixed-models at r-project.org> r-sig-mixed-models at r-project.org<mailto: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
> 
> _______________________________________________
> R-sig-mixed-models at r-project.org<mailto:R-sig-mixed-models at r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac