[BioC] affyio version update problem

[James W. MacDonald]

Hi Kim,

Kim Evans wrote:
> Hello
> 
> I have just managed to install Bioconductor on my Linux machine with the 
> help of my more computer savvy colleagues.  However, there was a 
> non-obvious problem that we needed to sort out.  I hope that by writing 
> this email I will save other people the time I've spent on it.
> 
> The problem was with the version of affyio that was being loaded.  The 
> information on the website about how to download Bioconductor does not 
> mention affyio.  What happened was that version 1.6 was automatically 
> found, but packages such as affy require version 1.8 or higher.  
> Presumably this is some problem with the way the references to updates 
> within Bioconductor are organised and updated.

How exactly did you install the packages? You are correct that the 
instructions don't directly mention affyio, but a simple

source("http://www.bioconductor.org/biocLite.R")
biocLite()

should have installed affy and the correct version of affyio.

Best,

Jim


> 
> Hope this is useful in making the download smoother for people.
> 
> Best wishes
> 
> Kim Evans
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623