installing lme4.0 on OS X 10.9

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
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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