[BioC] getting closer on YEAST 2.0 annotation...

[Jacob Michaelson]

I've gotten closer to getting a working yeast annotation package for 
the Affymetrix YEAST 2.0 chip.  I was able to procure the proper ORF 
ids and the probe ids, and from there I used yeastPkgBuilder within 
AnnBuilder to create a package.  It ran for a few hours and terminated 
with the following error:

Error in readLines(con) : cannot open the connection

 From what I can tell, it got most (if not all) of the probes processed. 
  I tried installing the package from the shell using

R CMD INSTALL YEAST2

YEAST2 is the name I gave to the package.  I get the error:

WARNING: invalid package 'YEAST2'
ERROR: no packages specified

I know it's there, it just doesn't think the directory is a valid 
package (dir includes R, man, data subdirectories).  I also tired 
installing via the Mac OS X GUI, which also failed.

There was also an XML file made, which seems to contain all the proper 
annotation.  Is there any way to create an annotation package from this 
XML file?  Why even make the XML file? (Just curious).

Thanks in advance,

Jake Michaelson