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

From: Uwe Ligges <ligges_at_statistik.tu-dortmund.de>
Date: Mon, 31 May 2010 17:55:00 +0200

On 31.05.2010 14:03, 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.
>
> 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 ?

  1. If you upgraded, why to R-2.10.1. given R-2.11.1 has been released today? Hence my recommedndation is to go ahead for R-2.11.1
  2. After strating R say

update.packages(checkBuilt=TRUE)
and all your outdated packages will be updated for the current version of R.

Uwe Ligges

> Thank you in advance.
> Maura
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> tutti i telefonini TIM!
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> [[alternative HTML version deleted]]
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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Mon 31 May 2010 - 15:56:56 GMT

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