Dear Jonathan, the last solution worked perfectly! Thank you very very much!
Best, *Gustavo Burin Ferreira, **Msc.* Instituto de Biociências Universidade de São Paulo Tel: (11) 98525-8948 On Tue, May 27, 2014 at 6:30 PM, Jonathan Chang <[email protected]>wrote: > 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 <[email protected]> > 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 > > <[email protected]> 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 âdiversitreeâ > >> * removing > >> > â/Library/Frameworks/R.framework/Versions/3.1/Resources/library/diversitreeâ > >> > >> 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 > [[alternative HTML version deleted]]
_______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
