[BioC] problem in biomaRt: getBM(output="list")

[Georg Otto]

Hi,

I have encountered a problem in biomaRt which is not serious, but kind
of annoying...

The atribute "zfin_xpat" (and maybe others) causes an error when the
output option "list" is chosen.

For example:

library(biomaRt)
ensembl<-useMart("ensembl", dataset="drerio_gene_ensembl")

# this works:

> getBM(attributes=c("zfin_xpat"), filters="affy_zebrafish", values=c("Dr.12.1.S2_at","Dr.12259.1.S1_at", "Dr.13845.1.A1_at"), mart=ensembl)
             zfin_xpat
1    ZDB-GENE-031008-1
2 ZDB-GENE-040426-1778
3 ZDB-GENE-040426-1778


# this does not work:

> getBM(attributes=c("zfin_xpat"), filters="affy_zebrafish", values=c("Dr.12.1.S2_at","Dr.12259.1.S1_at", "Dr.13845.1.A1_at"), mart=ensembl, output="list")
Error in read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "",  : 
	no lines available in input
> traceback()
4: stop("no lines available in input")
3: read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "", 
       as.is = TRUE)
2: getBM(attributes = attributes[j], filters = filters, values = values[k], 
       mart = mart)
1: getBM(attributes = c("zfin_xpat"), filters = "affy_zebrafish", 
       values = c("Dr.12.1.S2_at", "Dr.12259.1.S1_at", "Dr.13845.1.A1_at"), 
       mart = ensembl, output = "list")


> sessionInfo()
R version 2.4.0 (2006-10-03) 
powerpc-apple-darwin8.8.0 

locale:
C

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

other attached packages:
biomaRt   RCurl     XML 
"1.8.1" "0.8-0" "1.3-2" 

I think that this problem did not occur in the Ensembl release before
the current one. Any idea what is going on?

Best,

Georg