[BioC] Problems accessing Ensembl archive 59 with EnsEMBL

[Rhoda Kinsella]

Hi Aedin
The host name in the registry is incorrect. I have reported this issue  
to the Ensembl webteam and we will try to fix it as soon as possible.  
Thank you for reporting this and apologies for any inconvenience.
Rhoda

On 1 Dec 2010, at 21:21, aedin culhane wrote:

> Dear BioC Users (and Steffen)
> Whilst my script is working successfully to access older archives of  
> EnsEMBL, I can't access EnsEMBL 59.  I'd be grateful if you could  
> help me determine what the problem is.  Whilst useMart works,  
> listDatasets return no datasets in EnsEMBL59 mart.
>
> #----------
> #EnsEMBL Archive URLS
> #-----------
> urls= list( EnsEMBL57= "mar2010.archive.ensembl.org",
> 	    EnsEMBL58= "may2010.archive.ensembl.org",
> 	    EnsEMBL59= "aug2010.archive.ensembl.org")
>
>
>
> #----------
> #Quick Check Script to see problem with EnsEMBL 59
> #-----------
> for (EnsEMBLarchiveURL in urls) {
>    print(EnsEMBLarchiveURL)
>
>    ## Quick check marts ok
> print(listMarts(host=EnsEMBLarchiveURL,path="/biomart/ 
> martservice",archive=FALSE)[1:2,])
>
>
>    mart = useMart("ENSEMBL_MART_ENSEMBL",  
> host=EnsEMBLarchiveURL,path="/biomart/martservice",archive=FALSE)
>    datasets <- listDatasets(mart)
>
>    ## Quick check datasets ok
>    print(dim(datasets))
>    }
>
> mart<-useDataset("hsapiens_gene_ensembl",mart)
>
>
> [1] "mar2010.archive.ensembl.org"
>               biomart              version
> 1 ENSEMBL_MART_ENSEMBL     Ensembl Genes 57
> 2     ENSEMBL_MART_SNP Ensembl Variation 57
> [1] 51  3
> [1] "may2010.archive.ensembl.org"
>               biomart              version
> 1 ENSEMBL_MART_ENSEMBL     Ensembl Genes 58
> 2     ENSEMBL_MART_SNP Ensembl Variation 58
> [1] 51  3
> [1] "aug2010.archive.ensembl.org"
>               biomart              version
> 1 ENSEMBL_MART_ENSEMBL     Ensembl Genes 59
> 2     ENSEMBL_MART_SNP Ensembl Variation 59
> [1] 0 3
> >
> > mart<-useDataset("hsapiens_gene_ensembl",mart)
> Error in useDataset("hsapiens_gene_ensembl", mart) :
>  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct  
> dataset names can be obtained with the listDatasets function.
>
>
>
> Thanks a million
> Aedin
>
>
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i486-pc-linux-gnu (32-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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.6.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.4-3  tools_2.12.0 XML_3.2-0
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.