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

[Georg Otto]

Hi Steffen,

thanks for your help and for dendim me the fix, but unfortunately it
does not work:

> library(biomaRt)
Loading required package: XML
Loading required package: RCurl
> ensembl<-useMart("ensembl", dataset="drerio_gene_ensembl")
Error in getClass("CURLHandle") : "CURLHandle" is not a defined class
> traceback()
8: stop(gettextf("\"%s\" is not a defined class", Class), domain = NA)
7: getClass("CURLHandle")
6: .Call("R_curl_easy_init", PACKAGE = "RCurl")
5: getCurlHandle()
4: curlPerform(curl = curl, .opts = opts)
3: getURL(paste(host, "?type=registry&requestid=biomaRt", sep = ""))
2: listMarts(host = host, includeHosts = TRUE)
1: useMart("ensembl", dataset = "drerio_gene_ensembl")

> 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 
"1.9.14"  "0.8-0"  "1.3-2" 


Obviously there is a problem with the class CURLHandle. Is there a way
to fix that?

Cheers,

Georg


Steffen Durinck <durincks at mail.nih.gov> writes:

> Hi Georg,
>
> You found a bug and I've fixed it.  The changes have been committed to 
> the repository.
> (I will send you a new build shortly)
>
> Thanks for reporting this.
>
> best,
> Steffen
>
> Georg Otto wrote:
>> 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
>>
>> _______________________________________________
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>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>   
>
>
> -- 
> Steffen Durinck, Ph.D.
>
> Oncogenomics Section
> Pediatric Oncology Branch
> National Cancer Institute, National Institutes of Health
> URL: http://home.ccr.cancer.gov/oncology/oncogenomics/
>
> Phone: 301-402-8103
> Address:
> Advanced Technology Center,
> 8717 Grovemont Circle
> Gaithersburg, MD 20877
>
> _______________________________________________
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>

-- 

Georg Wilhelm Otto

Max-Planck-Institute for Developmental Biology

georg.otto at tuebingen.mpg.de