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

Mon Feb 10 19:26:01 CET 2014

Thank you!  Installing gfortran-4.2.3.pkg fixed things.  FWIW, it was indeed the most recent build of R that I had installed.

So that I (and perhaps other list members) understand the issues more completely: one thing that was very confounding to me is that installing gcc49 via MacPorts *does* provide a Fortran compiler, which goes in /opt/local/bin/gfortran.  However, I couldn’t figure out how to get R to use this compiler.  Perhaps this requires properly setting variables in ~/.R/Makevars, but I couldn’t figure out what the proper settings would be.  Do you have any guidance on this?

Best & thanks once more.

Roger

On Feb 10, 2014, at 11:08 AM, Simon Urbanek <simon.urbanek at r-project.org> wrote:

> 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
>> 
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