[Phylobase-devl] Finally!!

Jim Regetz regetz at nceas.ucsb.edu
Mon Aug 24 22:06:38 CEST 2009

Peter D. Cowan wrote:
> The Mac OS X build finally completed!! Would someone with a mac running 10.4, and R 2.9.2 please confirm that the following works.
> install.packages("phylobase", type="mac.binary", repos="http://R-Forge.R-project.org")

I just did some testing on a PowerPC Mac running OS X 10.4 and R 2.9.2.

First of all, after installing Xcode 2.5.0 Developer Tools on this 
otherwise clean test machine, the *source* installation of phylobase 
went without a hitch.

Unfortunately, the binary install didn't work. However, the issue I 
encountered seems to involve the architecture rather than the OS 
version. The installation step itself doesn't actually produce any 
errors or warnings, but when loading the package I get this:

 > library(phylobase)
Error: package "phylobase" is not installed for 'arch=ppc'

After surveying a few other R-Forge packages and their corresponding Mac 
build logs, I wonder if there is some problem with universal builds of 
R-Forge packages containing C++ code? I'm speculating, but I discovered 
two other packages (rgl and RInline) that produce this same arch=ppc 
error when I attempted to load them, and both (like phylobase) include 
C++ code. Moreover, the R-Forge build logs for several packages having 
only C/Fortran code report cpp/gfortran compiler statements targeting 
both i386 and ppc architectures, whereas only i386 shows up in g++ 
statements in the R-Forge build logs of phylobase, rgl, and RInline. (I 
should point out that some of the packages on R-Forge with only 
C/Fortran code also failed to load on this machine after installing from 
binary, but with completely different errors.)

One bit of potentially good news is that the rgl binary on CRAN 
installed fine for me, so this whole problem might also be a non-issue 
for phylobase on CRAN as opposed to R-Forge.

As for binary installation on an Intel Mac, I don't have one that I can 
readily downgrade to OS X 10.4 for testing. But frankly, given that the 
build itself seems to succeed on all tested platforms now, I think the 
odds are pretty good that CRAN will produce working binaries. Just don't 
quote me on that :)


> We may close #269 yet.
> Peter
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