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

[Mark Robinson]

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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