[BioC] Bioconductor and R 2.7

[Patrick Aboyoun]

The updated BioC 2.2 Windows binary packages, along with the source 
packages and Mac OS X binary packages, are now available from 
http://bioconductor.org/packages/2.2/bioc. You can obtain them, as 
usual, through the biocLite function when using R 2.7.0.


Cheers,
Patrick



Martin Morgan wrote:
> 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
>>>
>>> _______________________________________________
>>> 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
>>>   
>>>       
>> 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
>>     
>
>