[Bioc-devel] Parsing Error for UCSC Table

[Dario Strbenac]

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