sorry Wolfgang, here it is.
BTW, I just tried and it works today.
Thanks
Giovanni

library(biomaRt)

mart<-useMart("ensembl")

mart <- useDataset(dataset = "celegans_gene_ensembl", mart = mart)


wormids<-c("ZK666.6","Y41C4A. 
11","T02G5.7.1","K08F4.7","A_12_P11025","ZC410.5b","C32H11.2","F54D11.1" 
)
getBM (attributes=c 
("wormbase_gene","go_description"),filter="wormbase_gene",values=wormids 
,mart=mart)->gobiomart
Error: ncol(result) == length(attributes) is not TRUE
 >

Thank you very much
Giovanni


debug(getBM)
[...]
Browse[1]>
debug: xmlQuery = paste("<?xml version='1.0' encoding='UTF-8'?><! 
DOCTYPE Query><Query  virtualSchemaName = 'default' count = '0'>  
<Dataset name = '",
     mart@dataset, "'>", sep = "")
Browse[1]>
debug: attributeXML = paste("<Attribute name = '", attributes, "'/>",
     collapse = "", sep = "")

 > sessionInfo()
R version 2.1.0, 2005-05-12, 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"  "0.6-1" "0.99-6"  "1.1.7"  "1.6.3"  "2.0.8" "1.5.12"
 >



On Mar 30, 2006, at 7:19 AM, Wolfgang Huber wrote:

> Dear Giovanni,
>
> can you send us a sufficient code example to reproduce this error  
> please? Otherwise nobody can really do anything about your problem.
> I.e. how did you obtain your "mart" object?
>
>  Best
>  Wolfgang
>
> Giovanni Coppola wrote:
>> Hello Wolfgang,
>> I am actually getting a different error now... the wormids list  
>> is  usually much longer.
>>  > wormids<-c("ZK666.6","Y41C4A.  
>> 11","T02G5.7.1","K08F4.7","A_12_P11025","ZC410.5b","C32H11.2","F54D11 
>> .1" )
>>  > getBM (attributes=c  
>> ("wormbase_gene","go_description"),filter="wormbase_gene",values=worm 
>> ids ,mart=mart)->gobiomart
>> Error: ncol(result) == length(attributes) is not TRUE
>>  >
>> Thank you very much
>> Giovanni
>> debug(getBM)
>> [...]
>> Browse[1]>
>> debug: xmlQuery = paste("<?xml version='1.0' encoding='UTF-8'?><!  
>> DOCTYPE Query><Query  virtualSchemaName = 'default' count = '0'>   
>> <Dataset name = '",
>>     mart@dataset, "'>", sep = "")
>> Browse[1]>
>> debug: attributeXML = paste("<Attribute name = '", attributes, "'/>",
>>     collapse = "", sep = "")
>>  > sessionInfo()
>> R version 2.1.0, 2005-05-12, 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"  "0.6-1" "0.99-6"  "1.1.7"  "1.6.3"  "2.0.8" "1.5.12"
>>  >
>> On Mar 24, 2006, at 10:26 AM, Wolfgang Huber wrote:
>>> 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=wo 
>>>> rm ids ,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"
>
>
> -- 
> Best regards
>   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
> -------------------------------------


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