[BioC] Problems accessing Ensembl archive 59 with EnsEMBL

[aedin culhane]

Hi Rhonda
Thanks for your reply. Can I use a different URL in the interim?
Aedin

On 12/02/2010 04:16 AM, Rhoda Kinsella wrote:
> 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.
>