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 <[email protected]> wrote: > I'm forwarding this to R-sig-Mac. > > Tim Cole > -- > [email protected]<mailto:[email protected]> 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 > <[email protected]<mailto:[email protected]>> > To: Levy, Roger <[email protected]<mailto:[email protected]>> > Cc: "=?utf-8?Q?r-sig-mixed-models=40r-project.org?=" > <[email protected]<mailto:[email protected]>> > Subject: Re: [R-sig-ME] installing lme4.0 on OS X 10.9 > Message-ID: > <[email protected]<mailto:[email protected]>> > 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 > [email protected]<mailto:[email protected]> | Website | > Google Scholar > -------------------------------------------------------------------------------------------------------------- > From: Levy, Roger [email protected]<mailto:[email protected]> > Reply: Levy, Roger [email protected]<mailto:[email protected]> > Date: February 9,2014 at 23:41:48 > To: Tobias Heed [email protected]<mailto:[email protected]> > Cc: [email protected]<mailto:[email protected]> > [email protected]<mailto:[email protected]> > 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 > <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> > Reply: Levy, Roger [email protected]<mailto:[email protected]> > Date: February 7,2014 at 20:59:11 > To: [email protected]<mailto:[email protected]> > [email protected]<mailto:[email protected]> > 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 > > _______________________________________________ > [email protected]<mailto:[email protected]> > mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
