Hi Tommaso,

This is a recently discovered error and the BioMart people are looking into
it.
I've CC'd the bioconductor email list to let others know about the solution
below.
You need to query the ensembl BioMart directly at Ensembl as follows:

ensembl =
useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="
www.ensembl.org")
protein =
getBM(c("entrezgene","peptide"),filters="entrezgene",values=c(100, 5728),
mart=ensembl)

> protein
  entrezgene
1        100
2        100
3        100
4       5728
5       5728
6        100
7        100





                   peptide
1

MAQTPAFDKPKVELHVHLDGSIKPETILYYGRRRGIALPANTAEGLLNVIGMDKPLTLPDFLAKFDYYMPAIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVEPIPWNQAEGDLTPDEVVALVGQGLQEGERDFGVKARSILCCMRHQPNWSPKVVELCKKYQQQTVVAIDLAGDETIPGSSLLPGHVQAYQEAVKSGIHRTVHAGEVGSAEVVKEAVDILKTERLGHGYHTLEDQALYNRLRQENMHFEAQK*
2




MAQTPAFDKPKVELHVHLDGSIKPETILYYGRRRGIALPANTAEGLLNVIGMDKPLTLPDFLAKFDYYMPAIARL*
3

Cheers,
Steffen



On Thu, May 9, 2013 at 6:28 AM, Tommaso Leonardi <tl344@ebi.ac.uk> wrote:

> Dear Steffen,
> My name is Tom and I'm a student in the Enright group at EBI. I've
> just come across this error while going through one of the examples in
> the biomaRt vignette:
>
> > library("biomaRt")
> > ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
> > protein = getSequence(id=c(100,
> 5728),type="entrezgene",seqType="peptide", mart=ensembl)
> Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,
>  :
>   Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Can't create/write to file
> '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2)
>
> I'm not sure if this is due to a mistake I make or if it's a bug. Any
> info is very appreciated :)
> The sessionInfo is reported below.
>
> Thank you very much in advance and best regards
> tom
>
>
>
> > sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.16.0       BiocInstaller_1.10.1
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.95-4.1 tools_3.0.0    XML_3.95-0.2
>
>
>
> --
> Tommaso Leonardi - PhD student
> Enright group (EMBL-EBI) and
> Pluchino group (John van Geest Centre for Brain Repair)
> EMBL-EBI, Wellcome Trust Genome Campus
> Hinxton, CB10 1SD
> UK
>

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