On Mon, May 31, 2010 at 8:03 AM, <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.
>
>
As Heidi suggested, how did you check to see if you were connected to the
internet?  And was the BioMart service up and how did you check?


> 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 ?
>
>
Read this page.

http://bioconductor.org/docs/install/

If you have problems after following the instructions, please follow the
instructions in the posting guide and ask your question again.

Also, note that the newest version of R is 2.11 and not 2.10.1 Patched.

Sean

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