[BioC] Bioconductor and R 2.7

[Martin Morgan]

Hi Christian...

Christian Kohler <Christian.Kohler at klinik.uni-regensburg.de> writes:

> Wolfgang Huber wrote:
>> 29/04/2008 16:59 Steve Lianoglou a écrit

>>> Just out of curiosity, is it safe/recommended to upgrade to the new R
>>> 2.7.0 release when it says on the bioconductor website that that "This
>>> [bioconductor] release is designed for R 2.6.1"?

>> just don't try to carry over your installed packages from the 2.6.1
>> installation to the 2.7 one - please install all packages from scratch
>> using biocLite (http://www.bioconductor.org/download), which
>> automatically takes care of release version synchronisation between R
>> and Bioconductor.

> just out of personal interest: is the following error due to the fact
> that Bioconductor 2.2 is not yet officially released?
>
>>source("http://www.bioconductor.org/biocLite.R")
>> biocLite("Biobase")
> Running biocinstall version 2.2.7 with R version 2.7.0
> Your version of R requires version 2.2 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using 'XXX'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   package 'Biobase' is not available

There is a server issue at the Bioconductor web site. This will be
addressed as soon as possible.

Martin

>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i686-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
>
>
> Best,
> Christian
>
>
> -- 
>
> Christian Kohler
> Institute of Functional Genomics
> Computational Diagnostics
> University of Regensburg (BioPark I)
> D-93147 Regensburg (Germany)
>
> Tel. +49 941 943 5055
> Fax  +49 941 943 5020
> christian.kohler at klinik.uni-regensburg.de
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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