[Phylobase-devl] Urgent! problems with installing

Marguerite Butler mbutler at hawaii.edu
Wed Jul 2 11:23:30 CEST 2008

Hi Everyone,

For a brief while, all was fine in Mac binary land. But alas! No more...

Is anyone else having problems with R 2.7.1 or 2.7.0? I have found  
that read.nexus from ape does not work, as well as some odd NA-remove  
behavior in some statistical function.   So I've decided to remain  
downgraded to R 2.6.2 (patched).

The binaries were available on the r-forge site for a while, but not  
anymore. But my problem is that I can't even install from source.  
When I did R CMD check on the package, I get one warning:

* checking if this is a source package ... WARNING
Subdirectory 'pkg/src' contains object files.

I found "phylobase.so" in pkg/src. Is this supposed to be there? It  
might be the culprit because the error I get when I try to load  
phylobase is:

 > require(phylobase)
Loading required package: phylobase
Error in dyn.load(file, ...) :
   unable to load shared library '/Library/Frameworks/R.framework/ 
libs/i386/phylobase.so, 6): Library not loaded: /Library/Frameworks/ 
   Referenced from: /Library/Frameworks/R.framework/Resources/library/ 
   Reason: image not found

Which doesn't make a whole lot of sense since I'm installing from  
source on R 2.6.2.

So I went back and removed the "phylobase.so" from the pkg/src  
directory (the version I got from the svn repository -- revision  
192), and tried rebuilding. It passed the check this time, so I  
installed. But when I try loading, I still get the same error above  
from my require(phylobase) command??

Has anyone else had problems?

I don't think it's entirely a 2.6.2 issue because I don't think it's  
working for the 2.7.X versions either, otherwise wouldn't there be  
binaries available?

I am preparing for the NESCENT course, so this is pretty urgent. Any  
help would be greatly appreciated.

Marguerite A. Butler
Department of Zoology
University of Hawaii
2538 McCarthy Mall, Edmondson 259
Honolulu, HI  96822

Phone: 808-956-4713
FAX:   808-956-9812
Dept: 808-956-8617

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