[BioC] error when using trackNames function in rtracklayer

LiGang luzifer.li at gmail.com
Wed Jul 1 10:15:34 CEST 2009



=================================================
> library(rtracklayer)
Loading required package: RCurl
Loading required package: bitops

> browserSession("UCSC")->ex1


> str(ex1)
Formal class 'UCSCSession' [package "rtracklayer"] with 3 slots
  ..@ url  : chr "http://genome.ucsc.edu/cgi-bin/"
  ..@ hguid: num 3.1e+08
  ..@ views:<environment: 0x05a22d7c>



> trackNames(ex1)
Error in if (level > 2) stop("Failed to Parse HTML [", line, ":", col,  : 
  argument is of length zero



> traceback()
14: function (msg, code, domain, line, col, level, filename) 
    {
        if (level > 2) 
            stop("Failed to Parse HTML [", line, ":", col, "]: ", 
                msg)
    }(character(0), NULL, NULL, NULL, NULL, NULL, NULL)
13: .Call("RS_XML_ParseTree", as.character(file), handlers,
as.logical(ignoreBlanks), 
        as.logical(replaceEntities), as.logical(asText), as.logical(trim), 
        FALSE, FALSE, as.logical(isURL), FALSE, as.logical(useInternalNodes), 
        TRUE, FALSE, FALSE, as.character(encoding), as.logical(useDotNames), 
        xinclude, error, PACKAGE = "XML")
12: htmlTreeParse(str, asText = TRUE, useInternalNodes = TRUE, error =
htmlErrorHandler)
11: withCallingHandlers(expr, warning = function(w) invokeRestart
("muffleWarning"))
10: 
suppressWarnings(htmlTreeParse(str, asText = TRUE, useInternalNodes = TRUE, 
        error = htmlErrorHandler))
9: htmlParse(out)
8: httpGet(ucscURL(object, key), .form, ..., cookie = ucscCookie(object))
7: ucscGet(object, "tracks", form)
6: .local(object, ...)
5: ucscTracks(object)
4: ucscTracks(object)
3: .local(object, ...)
2: trackNames(ex1)
1: trackNames(ex1)


> sessionInfo()
R version 2.9.1 (2009-06-26) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;
LC_CTYPE=English_United States.1252;
LC_MONETARY=English_United States.1252;
LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
[1] rtracklayer_1.4.0 RCurl_0.98-1      bitops_1.0-4.1   

loaded via a namespace (and not attached):
[1] Biobase_2.4.1     Biostrings_2.12.7 BSgenome_1.12.3   IRanges_1.2.3    
tools_2.9.1       XML_2.5-3



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