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

[Steffen Durinck]

Hi Georg,

It looks like this is an error coming from the RCurl package rather than 
from biomaRt.
I've just installed the same version of RCurl as yours but can not 
replicate the error and everything works fine on my Linux box.
I'll try to replicate your error on a mac later today, hopefully this 
will give us some hints.

best,
Steffen

Georg Otto wrote:
> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> 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