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 <[email protected]> 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 <[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 > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
