[BioC] after updating biomaRt cannot connect any more

[Heidi Dvinge]

On 31 May 2010, at 13:03, <mauede at alice.it> <mauede at alice.it> wrote:

> I recently updated R  2.10.1 Patched (2010-02-20 r51163)
> This morning I reinstalled biomaRt using biocLite.
> Now I can no more connect to biomaRt and even the following  
> instruction is hanging  for a while until
> the same error message pops up.
>> listMarts()
> Error in value[[3L]](cond) :
>   Request to BioMart web service failed. Verify if you are still  
> connected to the internet.  Alternatively the BioMart web service  
> is temporarily down.
>
Did you check this as suggested in the error message? Currently, when  
I try http://www.biomart.org/ it doesn't seem to work.

Regards
\Heidi

> I checked my command syntax  and got the following message:
>> library(help=biomaRt)
> Warning messages:
> 1: package 'JavaGD' was built under R version 2.9.0 and help may  
> not work correctly
> 2: package 'Biobase' was built under R version 2.9.0 and help may  
> not work correctly
> 3: package 'Biostrings' was built under R version 2.9.0 and help  
> may not work correctly
> 4: package 'IRanges' was built under R version 2.9.0 and help may  
> not work correctly
> 5: package 'CORNA' was built under R version 2.9.0 and help may not  
> work correctly
> 6: package 'GEOquery' was built under R version 2.9.0 and help may  
> not work correctly
> 7: package 'microRNA' was built under R version 2.9.0 and help may  
> not work correctly
> 8: package 'Rlibstree' was built under R version 2.9.0 and help may  
> not work correctly
>>
> I am stuck.
> Which packages am I supposed to install again ?  Maybe shall I get  
> rid of R  2.10.1 Patched
> and restart from scratch ?
>
> Thank you in advance.
> Maura
>
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> tutti i telefonini TIM!
>
>
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