[BioC] UCSC rtracklayer error "transfer closed with outstanding read data remaining"

[Keith Satterley]

Hi mark,

I just tried your commands on my Windows box. Worked fine. I was 
actually distracted doing something else, but it had finished when I 
looked back 15 minutes later.

knownGene had 66803 elements.

I was wondering why you are using hg18 when hg19 is available.

my sessionInfo is:

R version 2.12.0 Patched (2010-11-26 r53670)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252  
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                     
[5] LC_TIME=English_Australia.1252   

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

other attached packages:
[1] rtracklayer_1.9.11 RCurl_1.4-4.1      bitops_1.0-4.1     

loaded via a namespace (and not attached):
[1] Biobase_2.9.2        Biostrings_2.17.48   BSgenome_1.17.7    
[4] GenomicRanges_1.1.38 IRanges_1.7.40       XML_3.2-0.1 

My R is the latest November release, not sure if that has had any effect 
or the fact that it was done at a different time (I did it at about 
8:45pm (Australian EST = GMT+10) on Saturday Dec. 4

cheers,

Keith

========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
email:keith at wehi.edu.au
=======================



Mark Robinson wrote:
> Hi all.
>
> Can someone advise on my issue below?  I can't seem to grab the UCSC table 'knownGene', but it works for 'ensGene'.  Is this a timeout error?  'knownGene' is only marginally larger (in rows) than 'ensGene'.  Any solution?
>
> Thanks!
> Mark
>
>   
>> library(rtracklayer)
>>     
> Loading required package: RCurl
> Loading required package: bitops
>   
>> session <- browserSession("UCSC")
>> genome(session) <- "hg18"
>> q <- ucscTableQuery(session, "knownGene")
>> knownGene <- getTable(q)
>>     
> Error in curlPerform(url = url, headerfunction = header$update, curl = curl,  : 
>   transfer closed with outstanding read data remaining
>   
>> traceback()
>>     
> 11: .Call("R_curl_easy_perform", curl, .opts, isProtected, .encoding, 
>         PACKAGE = "RCurl")
> 10: curlPerform(url = url, headerfunction = header$update, curl = curl, 
>         .opts = .opts)
> 9: getURLContent(uri, .opts = .opts, .encoding = .encoding, binary = binary, 
>        curl = curl)
> 8: getForm(url, .params = .form, .opts = list(..., useragent = "rtracklayer"))
> 7: httpGet(ucscURL(object, key), .form, ..., cookie = ucscCookie(object))
> 6: ucscGet(browserSession(query), "tables", c(ucscForm(query, tracks = tracks), 
>        ...), .parse = .parse)
> 5: ucscTableGet(object, !is.null(followup), hgta_doTopSubmit = "get output", 
>        hgsid = hgsid)
> 4: ucscExport(object)
> 3: .local(object, ...)
> 2: getTable(q)
> 1: getTable(q)
>   
>> q <- ucscTableQuery(session, "ensGene")
>> ensGene <- getTable(q)
>>
>> dim(ensGene)
>>     
> [1] 63280    16
>   
>> sessionInfo()
>>     
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] rtracklayer_1.10.3 RCurl_1.5-0        bitops_1.0-4.1    
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.10.0      Biostrings_2.18.0   BSgenome_1.18.0    
> [4] GenomicRanges_1.2.0 IRanges_1.8.0       XML_3.2-0    
>
>
> ------------------------------
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: mrobinson at wehi.edu.au
> e: m.robinson at garvan.org.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> ------------------------------
>
>
> ______________________________________________________________________
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