Re: [R] [BioC] after updating biomaRt cannot connect any more

From: Heidi Dvinge <heidi_at_ebi.ac.uk>
Date: Mon, 31 May 2010 13:28:04 +0100

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
>
>
>
>
>
>
>
> tutti i telefonini TIM!
>
>
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>
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