[BioC] bioconductor affy lib with R 2.0.1

[Seth Falcon]

"Susan J. Miller" <sjmiller at email.arizona.edu> writes:
>> This looks like the type of error one would see if R is finding an
>> old
>> version of Biobase on the system.  Is that possible?
>
> In the DESCRIPTION file for Biobase it says:
>
> Package: Biobase
[snip]
> Built: R 1.9.1; sparc-sun-solaris2.8; 2005-01-24 16:31:07; unix

So this is a stale version of the Biobase package and this is the
cause of your problem.

>> Did you install over an existing R install?
>
> Yes, I did (R version 1.9.1).  Is there some sort of cleanup I should
> have done?

We need better documentation on this.  Since you had Bioconductor
installed already, I think using update.packages2 from reposTools
would have helped.  

At this point, I'm not sure what the best course of action is because
you may have a mix of new and old?  Here are things you could try:

* Try to use update.packages2

* To be safe, you can remove all Bioconductor packages from your
  package library (just rm -r the package directories).  Be careful
  not to remove the packages that come with R.

* Another option would be to nuke the package library entirely and
  reinstall R and then run getBioC.

We are working on making this sort of upgrade process *much* easier
and less error prone in the next release (coming in mid May).


Best,

+ seth