[BioC] biomaRt does not load archived Ensembl Genes database anymore.

[J.H. Brandsma]

Hi there!

I've run into a problem with biomaRt and the biomart on ensembl.org. When I try to load the Ensembl Genes 67 I run into trouble.  Until a month a go it did load like it should. The strange thing is when I use the same code but change the host from  "may2012.archive.ensembl.org" to "www.ensembl.org" it loads without any trouble. Other archived hosts also do not load, only the most recent version seems to work. I cannot use the most recent version, because it is based on mm10. 

In the script below I first show that the most recent Ensembl Genes 69 does load and last that the Ensembl Genes 67 does not. 

Does anyone have any idea what is going on and can anyone suggest a possible solution? 

Thank you in Advance,

Johan Brandsma
Erasmus MC, Rotterdam, The Netherlands.

> library(biomaRt)
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-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=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.10.0 rkward_0.5.6  

loaded via a namespace (and not attached):
[1] RCurl_1.95-3 tools_2.14.1 XML_3.95-0.1

> listMarts("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 69
2     ENSEMBL_MART_SNP  Ensembl Variation 69
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 69
4    ENSEMBL_MART_VEGA               Vega 49
5             REACTOME    REACTOME (CSHL US)
6                pride        PRIDE (EBI UK)
> mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", host="www.ensembl.org")

> listMarts("ENSEMBL_MART_ENSEMBL", host="may2012.archive.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 67
2     ENSEMBL_MART_SNP  Ensembl Variation 67
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 67
4    ENSEMBL_MART_VEGA               Vega 47
5             REACTOME    REACTOME (CSHL US)
6                pride        PRIDE (EBI UK)
> mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", host="may2012.archive.ensembl.org")
Error in read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "",  : 
  no lines available in input
Calls: useMart -> bmVersion -> read.table