[BioC] Ensembl websites offline for maintenance

[Robert Castelo]

Dear Rhoda,

i was unsuccessfully trying to connect to the human ensembl genes
dataset of the archived Ensembl release 63 and i just wondered whether
this problem has anything to do with your annoucement below or whether
i'm doing anything wrong. here is the code:

## following the example of page 15 of the biomaRt vignette
## adapted to the release 63
library(biomaRt)
listMarts(host="jun2011.archive.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 63
2     ENSEMBL_MART_SNP  Ensembl Variation 63
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 63
4    ENSEMBL_MART_VEGA               Vega 43
5             REACTOME              Reactome
6                pride        PRIDE (EBI UK)
ensembl63 <- useMart(host="jun2011.archive.ensembl.org",
biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
Error in useDataset(mart = mart, dataset = dataset, verbose =
verbose) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct
dataset names can be obtained with the listDatasets function.
sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets
methods  
[8] base     

other attached packages:
[1] Biobase_2.12.1 biomaRt_2.8.0 

loaded via a namespace (and not attached):
[1] RCurl_1.5-0 XML_3.4-0  


thanks!
robert.


On Thu, 2011-10-20 at 13:11 +0100, Rhoda Kinsella wrote:
> Dear all
> 
> All Sanger-based Ensembl websites and related services will go offline  
> around midday tomorrow, Friday 21st October until the evening of  
> Sunday 23rd October. This will affect the main Ensembl website,  
> archives, Pre! and beta. Mirror sites (US and Asia) will remain  
> available, but Sanger-dependent services, including BLAST and user  
> accounts, will be disabled.
> 
> For Ensembl BioMart users this will mean that you will not be able to  
> query the Ensembl marts from www.biomart.org or www.ensembl.org. You  
> will be able to access release 64 Ensembl marts via the mirrors at:
> 
> http://uswest.ensembl.org/index.html
> http://useast.ensembl.org/index.html
> http://asia.ensembl.org/index.html
> 
> 
> We hope that the datacentre restart will go smoothly and the sites  
> will be back online by Monday morning at the latest - if you find a  
> site is not working as expected by noon UK time, please let us know so  
> that we can investigate.
> 
> Please accept our apologies for any inconvenience caused.
> 
> 
> Regards
> Rhoda
> 
> 
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
> 
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