[BioC] Bioconductor and R 2.7

[Christian Kohler]

Wolfgang Huber wrote:
> 29/04/2008 16:59 Steve Lianoglou a écrit
>   
>> Hi all,
>>
>> I'm fairly new to R and completely new to bioconductor.
>>
>> 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"?
>>
>> Thanks,
>> -steve
>>     
>
> Hi Steve,
>
> 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.
>
> Best wishes
>  Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
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>   
Dear all,

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

> 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