[BioC] Ensembl websites offline for maintenance
Robert Castelo
robert.castelo at upf.edu
Thu Oct 20 16:17:57 CEST 2011
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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