Re: [R-sig-phylo] Installing diversitree on OS X Mavericks, R 3.1.0
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 - 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/
Re: [R-sig-phylo] Installing diversitree on OS X Mavericks, R 3.1.0
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/
Re: [R-sig-phylo] Installing diversitree on OS X Mavericks, R 3.1.0
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 jonathan.ch...@ucla.eduwrote: 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 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 - 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/
