[BioC] Bioconductor and R 2.7

[Christian Kohler]

Hallo Wolfgang,

thanks for your response.

The same problem occured on Mac OS X (Leopard) with R.app (2008/04/23)
as well:


> source("http://www.bioconductor.org/biocLite.R")
> biocLite("Biobase", type="source") # also with type="binary"
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 '~/Library/R/2.7/library'
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)
i386-apple-darwin8.10.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

loaded via a namespace (and not attached):
[1] tools_2.7.0


The same result after following your suggestion with R --vanilla.

I think, my last 'biocLite()'-try was on Monday and worked without any
problem.

Best,
Christian


Wolfgang Huber wrote:
> 30/04/2008 11:19 Christian Kohler a écrit
>   
>> 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
>>
>>     
>
> Dear Christian,
>
> biocLite has worked well for me for a number of installations of R 2.7
> recently, so the problem you report either popped up very, very recently
> (and is unintended), or it has to do with your local installation. Can
> you try with
>
>   R --vanilla
>
>
>   


-- 

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