Hello,
Obtaining the RefSeq table through the Table Browser at UCSC works. However,
using GenomicFeatures results in an error.
> tx19 <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene")
Download the refGene table ... Error in function (type, msg, asError = TRUE) :
Received problem 2 in the chunky parser
> traceback()
14: fun(structure(list(message = msg, call = sys.call()), class = c(typeName,
"GenericCurlError", "error", "condition")))
13: function (type, msg, asError = TRUE)
{
if (!is.character(type)) {
i = match(type, CURLcodeValues)
typeName = if (is.na(i))
character()
else names(CURLcodeValues)[i]
}
typeName = gsub("^CURLE_", "", typeName)
fun = (if (asError)
stop
else warning)
fun(structure(list(message = msg, call = sys.call()), class =
c(typeName,
"GenericCurlError", "error", "condition")))
}(56L, "Received problem 2 in the chunky parser", TRUE)
12: .Call("R_post_form", curl, .opts, .params, TRUE, matchPostStyle(style),
PACKAGE = "RCurl")
11: .postForm(curl, .opts, .params, style)
10: postForm(url, .params = .form, .opts = list(..., useragent = "rtracklayer"))
9: httpPost(ucscURL(object, key), .form, ..., cookie = ucscCookie(object))
8: ucscPost(browserSession(query), "tables", c(ucscForm(query, tracks =
tracks),
list(...)), .parse = .parse)
7: ucscTablePost(query, hgta_enteredUserRegionFile = upload,
hgta_enteredUserRegions = "",
hgta_doSubmitUserRegions = "submit", hgsid = hgsid)
6: .uploadTableBrowserRanges(object, hgsid)
5: ucscExport(object)
4: .local(object, ...)
3: getTable(query)
2: getTable(query)
1: makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene")
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] org.Hs.eg.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7
[4] GenomicFeatures_1.12.2 AnnotationDbi_1.22.6 Biobase_2.20.1
[7] GenomicRanges_1.12.4 IRanges_1.18.2 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] biomaRt_2.16.0 Biostrings_2.28.0 bitops_1.0-5
[4] BSgenome_1.28.0 RCurl_1.95-4.1 Rsamtools_1.12.3
[7] rtracklayer_1.20.4 stats4_3.0.1 tools_3.0.1
[10] XML_3.98-1.1 zlibbioc_1.6.0
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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