[BioC] Bioconductor and R 2.7

[Martin Morgan]

To follow up...

Some spring cleaning in preparation for the release was a little too
effective.

biocLite should now work for Linux and Mac packages; Windows packages
are in the process of being rebuilt. 

Thanks for alerting us to this problem.

Martin

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

> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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