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 didnt work. Unfortunately, I do not recall everything I tried back then. I do recall that the problem was that gcc doesnt 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 its 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 Ive 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, Im 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]]
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