[BioC] Problems with gcrma using latest version of R and Bioconductor

[James MacDonald]

Hi Sebastian,

I don't know if there is a method to check for mis-matched packages, but 
there is a simple way to update your packages so in truth there should 
be no need for such checking.

If you update your R version, all you need to do is then install all 
needed packages using biocLite().

If for whatever reason you haven't used biocLite() to install the 
packages, you can always use update.packages():

biocLite("Biobase") ##ensure Biobase is correct version
library(Biobase)
repos <- biocReposList()
update.packages(repos=repos, ask=FALSE)

If you follow either prescription then you should never have to worry 
about mis-matched packages. If you do something else, then you are on 
your own ;-D

Best,

Jim



Sebastian Bauer wrote:
> Hi James,
> 
> James W. MacDonald wrote:
>> Please always give us the output of sessionInfo() as well. Just 
>> telling us you have BioC 2.0 isn't sufficient. For instance, I get 
>> this to work:
> 
> Thanks for your quick reply. You sessionInfo() output gave me the hint 
> that I did not update some of the annotation packages whose existence I 
> wasn't  aware of (initially, I updated only the mouse4302 package) :) 
> After updating the rest, all seems to work again.
> 
> However, from an user's point of view, I would rather like to see an 
> appropriate error message coming up which complains about non-matching 
> versions of the required package. Is there such a mechanism in 
> Bioconductor/R?
> 
> Ciao,
> Sebastian

-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623