[Phylobase-devl] Urgent! problems with installing

[Marguerite Butler]

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/ 
Resources/library/phylobase/libs/i386/phylobase.so':
   dlopen(/Library/Frameworks/R.framework/Resources/library/phylobase/ 
libs/i386/phylobase.so, 6): Library not loaded: /Library/Frameworks/ 
R.framework/Versions/2.7/Resources/lib/libR.dylib
   Referenced from: /Library/Frameworks/R.framework/Resources/library/ 
phylobase/libs/i386/phylobase.so
   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
____________________________________________
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
http://www2.hawaii.edu/~mbutler
http://www.hawaii.edu/zoology/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.r-forge.r-project.org/pipermail/phylobase-devl/attachments/20080701/cce384af/attachment.htm