[BioC] problem upgrading limma on Windows Vista

James W. MacDonald jmacdon at med.umich.edu
Fri Mar 7 20:51:37 CET 2008

Hi Susan,

Usually this happens when you get a half-deleted package, often when 
there isn't anything in the e.g., <RHOME>/library/limma directory, but 
the directory still exists.

Check to see if there is a limma directory in your library directory, if 
so, delete it by hand and then try re-installing using biocLite().



Susan J. Miller wrote:
> 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
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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