Good afternoon,

I am contacting you for an information regarding biomaRt, I have already contacted the BioMart helpdesk but they suggested to email you, as this is probably a bug of the biomaRt package.

Every time I try to get annotation info on a SNP using biomaRt, the R console crashes. The session info are:

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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


And the commands that I use are:

library(biomaRt)
snp.db = useMart("ENSEMBL_MART_SNP",host="www.ensembl.org<http://www.ensembl.org>",dataset="hsapiens_snp")
variant = list(9,133271654)
var_info = getBM(c("chr_name","chrom_start","allele","minor_allele","minor_allele_freq"),c("chr_name","chrom_start"),variant,snp.db)

R always crashes at this point, also on other computers. I am using R 3.0.1 and the biomaRt package is up to date.

Where could the problem be?

Thanks a lot for the assistance!
Francesco Mazzarotto


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