[BioC] Problems accessing Ensembl archive 59 with EnsEMBL

[aedin culhane]

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