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

From: Uwe Ligges <ligges_at_statistik.tu-dortmund.de>
Date: Mon, 31 May 2010 17:56:13 +0200

On 31.05.2010 17:55, Uwe Ligges wrote:
>
>
> On 31.05.2010 14:03, mauede@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 and all your outdated packages will be updated for the current version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.

And DO NOT cross post (as I did while responding without paying attention to the list of CCs).

Uwe Ligges

> Uwe Ligges
>
>
>
>> Thank you in advance.
>> Maura
>>
>>
>>
>>
>>
>>
>>
>> tutti i telefonini TIM!
>>
>>
>> [[alternative HTML version deleted]]
>>
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R-help_at_r-project.org mailing list
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 - 15:59:29 GMT

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