error when using trackNames function in rtracklayer
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li lilingdu ▴ 450
@li-lilingdu-1884
Last seen 5.9 years ago
================================================= > 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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