Possibly a proxy issue?  I don't think I've seen that particular error
message.

On Fri, Dec 3, 2010 at 9:51 PM, Mark Robinson <mrobinson@wehi.edu.au> 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@wehi.edu.au
> e: m.robinson@garvan.org.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> ------------------------------
>
>
> ______________________________________________________________________
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