[BioC] Problems accessing Ensembl archive 59 with EnsEMBL

[Rhoda Kinsella]

Hi Aedin,
I'm afraid not but you can of course link to the current release 60 on www.ensembl.org 
  or www.biomart.org. The web team have assured me they will fix it as  
soon as possible.
Regards,
Rhoda


On 2 Dec 2010, at 15:20, aedin culhane wrote:

> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> Rhoda Kinsella Ph.D.
>> Ensembl Bioinformatician,
>> European Bioinformatics Institute (EMBL-EBI),
>> Wellcome Trust Genome Campus,
>> Hinxton
>> Cambridge CB10 1SD,
>> UK.
>>

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.