[BioC] problem upgrading limma on Windows Vista

[Susan J. Miller]

Perhaps someone has seen this behavior and can help:

I am working with a student who has a Windows vista laptop.  She had 
installed R 2.6.2 and Bioconductor.  When working with the swirl sample 
data set and trying to normalize within arrays, an error with the lowess 
function was occurring.  I checked the limma version and it was 2.9.7, 
so we tried to install limma 2.12, but got a warning that the prior 
version of limma cannot be removed.  Oddly, the machine is in a state 
such that if from the R GUI we choose Packages->Load Package, limma does 
not appear on the list (which makes sense because there is no limma 
folder in C:\Program Files\R\R-2.6.2\library).  Yet if we try to install 
limma, we see the 'cannot remove prior version' error.  We even 
uninstalled R and re-installed it, but the same problem with installing 
limma persists.

I guess I never should have joked early on that we could probably blame 
this problem on Vista...but it's looking like that may be the case.  Any 
ideas would be appreciated.

Thanks,

Susan J. Miller
Manager, Scientific Data Analysis
Biotechnology Computing Facility
Arizona Research Laboratories
(520) 626-2597