[BioC] Problems updating bioconductor

[Seth Falcon]

"M. Gonzalo Claros Díaz"  <claros at uma.es> writes:

> Hello all.
>
> I was using R 2.4x with Mac OSX without problems, but when I upgraded  
> to 2.5 I'm always having problems trying to update the libraries.
>
> When I write update.packages() I do not receive any news. When I know  
> that there is a new version of a library, I'm trying to install it  
> but I always have the message

If you are calling update.packages with no arguments, then you are
relying on the repos option (getOptions("repos")).  You haven't told
us what you have set there, but I suspect that may be related to the
message you are seeing.

I would recommend the following procedure to update:

1. Make sure Biobase is up-to-date.  You can check the version number
   against what is available on the website.  The current release
   version is Bioconductor 1.14.0.

2. Do this:

   library("Biobase")
   update.packages(repos=biocReposList())

> : unable to access index for repository http://www.bioconductor.org/ 
> packages/2.0/omegahat/bin/macosx/universal/contrib/2.5
>
> ¿Do someone know where is the problem o where must I change something  
> to avoid this?

We renamed our "omegahat" repository "extra" because it really was not
a mirror of the omegahat project's repository, but consists of extra
non-CRAN, non-BioC packages that are used by various BioC packages.

biocLite() and biocReposList() know about the change, but any
hard-coded URLs to the repositories would not (obviously) know abou
the change.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org