[BioC] Affy 1.5.8 functions not working on Mac OS X 10.3

[Chad Wayne]

It was recommended that I post this problem to the mailing list. I am 
unable to get affy to work, e.g. the library loads into R, but the 
functions don't seem to work. I was hoping someone may have seen this 
problem before and may have a solution. I am working in the correct 
working directory.

I am using version v2.0.1 of R with the default Bioconductor package 
installed. Current package of Affy is 1.5.8. I am using Mac OS X 10.3.7 
and running X11 (X11 1.0 - XFree86 4.3.0). This is a shared environment 
and all packages were installed in the top library, not in the User 
library.

On prompt:
 > load("/nnn/nnn/nnn/timecourse.RData")
 > library(affy)
Loading required package: Biobase
Loading required package: tools
Loading required package: reposTools
 > ReadAffy(widget=T)
Error: couldn't find function "ReadAffy"
 > ReadAffy()
Error: couldn't find function "ReadAffy"
 > pData(eset)
Error: couldn't find function "pData"

I've also attempted to "start from scratch" from the original .cel 
files and get the same type of error message that the function couldn't 
be found.

I have checked to ensure that affy is installed and loaded, and based 
on the Package Manager, it is .


I've also tried using limma (v1.8.10), and had no problems, other than 
I can't read in the eset.

 > packageDescription("limma", field="Version")
[1] "1.8.10"
 > packageDescription("affy", field="Version")
[1] "1.5.8"
 > version
          _
platform powerpc-apple-darwin6.8
arch     powerpc
os       darwin6.8
system   powerpc, darwin6.8
status
major    2
minor    0.1
year     2004
month    11
day      15
language R


Thanks for the assistance.

Chad Wayne

Chad M. Wayne, Ph. D.
Baylor College of Medicine