Actually I suppose the recommended course of action would be to just use the Snow Leopard version, which will probably work fine on Mavericks (and diversitree will have a pre-built binary from the R developers). First uninstall your current version of R with `sudo rm -rf /Library/Frameworks/R.framework/` then install this version: http://cran.rstudio.com/bin/macosx/R-3.1.0-snowleopard.pkg
Jonathan On Tue, May 27, 2014 at 2:21 PM, Jonathan Chang <jonathan.ch...@ucla.edu> wrote: > It looks like there's an issue with your install of Homebrew, since > installing those packages should also link them into the proper > directories. Try > > brew unlink gsl gcc fftw > brew link gsl gcc fftw > > These should run without error. If you can't link those packages then > it means you already have a previous non-Homebrew install of these > software. You can force it with `brew link --overwrite gsl` etc. but > this will probably lead to a horrifying frankeninstall and cause > further problems down the road. > > The other issue you have is that the gfortran in your PATH reports > version 4.8.2 but your (unlinked) Homebrew copy is version 4.8.3, > which is the one that you actually want. Again, this indicates a > previous non-Homebrew install of gfortran, which will cause software > installs to fail in exciting and unpredictable ways. > > If you are comfortable with reinstalling all of your software from > scratch I would recommend deleting everything in /usr/local/ to start > from a blank slate. > > Jonathan > > On Tue, May 27, 2014 at 1:47 PM, Gustavo Burin Ferreira > <ariete...@gmail.com> wrote: >> Dear John and list, >> >> I have tried to use your tutorial, but without success. I am getting the >> following error: >> >> ld: library not found for -lquadmath >> clang: error: linker command failed with exit code 1 (use -v to see >> invocation) >> make: *** [diversitree.so] Error 1 >> ERROR: compilation failed for package ‘diversitree’ >> * removing >> ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/diversitree’ >> >> I am not sure if it has any relation to the error, but after installing for >> the first time, when I try to run >> >> brew install gsl gcc fftw >> >> to check if the installation is there, I get the following error >> >> Warning: gsl-1.16 already installed, it's just not linked >> Warning: gcc-4.8.3 already installed, it's just not linked >> Warning: fftw-3.3.4 already installed, it's just not linked >> >> Also, when I run >> >> gfortran --version >> >> I get >> >> GNU Fortran (GCC) 4.8.2 >> >> I am having a really hard time installing diversitree on Mavericks. I hope >> there is a workaround or anything like that. >> >> Please let me know if you need any other information. >> >> Thank you all very much in advance for any help. >> >> Regards, >> >> Gustavo Burin Ferreira, Msc. >> Instituto de Biociências >> Universidade de São Paulo _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
