[BioC] R crash on getBM query

[Sean Davis]

Hi, Francesco.

If you could send the output of sessionInfo() after loading biomaRt,
that would be helpful.  Also, could you send the error output?  Note
that the biomaRt has been down at least intermittently for the last
day or so, so your query might not complete.  The error output will
hopefully help to determine what the issue is, though.

Sean


On Fri, May 17, 2013 at 11:27 AM, Mazzarotto, Francesco
<f.mazzarotto at imperial.ac.uk> wrote:
> 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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>
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