[BioC] getBM (biomaRt) sometimes returns NULL

[Wolfgang Huber]

Ciao Giovanni,

can you provide a script that allows us to reproduce this error?

In any case, I think getBM should produce a useful error message rather 
than just quietly returning NULL and we will fix this.

To be even more helpful, you could also say "debug(getBM)" before 
calling getBM, and report to us the content of "xmlQuery" and "postRes" 
after the call to the "postForm" function (this is the main action of 
the function getBM, when it talks to the Wormbase webservice).

Best wishes
  Wolfgang


-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber
-------------------------------------


Giovanni Coppola wrote:
> Hello everybody,
> I am using biomaRt to retrieve worm annotation.
> Sometimes (apparently unpredictably) I get a NULL output and a warning:
> 
>  > getBM (attributes=c 
> ("wormbase_gene","go_description"),filter="wormbase_gene",values=wormids 
> ,mart=mart)->gobiomart
> Warning message:
> getBM returns NULL. in: getBM(attributes = c("wormbase_gene",  
> "go_description"), filter = "wormbase_gene",
> 
> The exact same line works later. Has anyone experienced this? Is  
> there a timeout issue or something like that?
> 
> Thanks
> Giovanni
> 
> 
>  > sessionInfo()
> R version 2.2.1, 2005-12-20, powerpc-apple-darwin7.9.0
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> [7] "datasets"  "base"
> 
> other attached packages:
> biomaRt    RCurl      XML  convert   marray    limma  Biobase
> "1.5.12"  "0.6-0" "0.99-6"  "1.4.0"  "1.8.0"  "2.4.7"  "1.8.0"