On Feb 10, 2014, at 1:26 PM, Levy, Roger <[email protected]> wrote: > 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? >
The CRAN build is a native build of R and only supports native compilers. If you use MacPorts you're entirely on your own - you may want to use MacPorts R in that case or compile everything from sources accordingly. Cheers, Simon > 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
