[BioC] bioconductor affy lib with R 2.0.1
sfalcon at fhcrc.org
Thu Apr 7 19:00:32 CEST 2005
"Susan J. Miller" <sjmiller at email.arizona.edu> writes:
>> This looks like the type of error one would see if R is finding an
>> version of Biobase on the system. Is that possible?
> In the DESCRIPTION file for Biobase it says:
> Package: Biobase
> 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).
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