Making ape work on Mac OSX 10.8

ape 3.0.7 on Mac OSX 10.8 has some problems reading fasta files! read.dna doesn’t see “G” (???) and line endings are messed up.

From the internet (http://comments.gmane.org/gmane.comp.lang.r.phylo/2509):

Feb 6, 2013

“Hi Rupert, The Mac version of ape on CRAN is not correct and has a few bugs particularly in read.dna(). Another problem is that “G” is not read (but “g” is). This does not affect the Windows version nor the sources. A solution for Mac users is re-install from the sources. Another one is to use the code of read.dna() from a previous release of ape.   I’m waiting for other tests and feed-back before releasing ape 3.0-8 (within one or two weeks).

Best, Emmanuel”

 Solution: install from source:

1. Install Xcode (from Mac App store, running OSX 10.8.2)

2. In Xcode, under “Preferences”, “Downloads”, select “Command Line Tools” install button

3. Still need gfortran, go to http://hpc.sourceforge.net/ and download http://prdownloads.sourceforge.net/hpc/gfortran-mlion.tar.gz?download (for Mountain Lion only).

In Terminal, cd to the Download folder:

gunzip gfortran-mlion.tar.gz

sudo tar -xvf gfortran-mlion.tar -C /.

4. In R Installer, select CRAN (sources) and install ape 3.0.8

5. It works!