I seem to be having an issue with Ucsctrack in GViz:

exfail=UcscTrack(track="CpG Islands", chromosome="chr6", genome="hg19",
start="chromStart", end="chromEnd", name="CpG Islands", from=31731740,
to=31736112)

Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function ".buildRange", for
signature "NULL", "logical", "logical", "NULL"

This occurs when I try to get an area where there are no annotations(i.e.
expected behavior is an empty object).  Is this a known bug, or am I doing
something horribly, horribly wrong?  I'm using the release version of Gviz.

traceback and sessionInfo included below.

Thanks,

Winston Timp

> traceback()
6: stop("unable to find an inherited method for function \"", fdef@generic,
       "\", for signature ", cnames)
5: function (classes, fdef, mtable)
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L)
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", sapply(classes, as.character),
               "\"", collapse = ", ")
           stop("unable to find an inherited method for function \"",
               fdef@generic, "\", for signature ", cnames)
       }
       else stop("Internal error in finding inherited methods; didn't
return a unique method")
   }(list("NULL", "logical", "logical", "NULL"), function (range,
       start, end, width, ...)
   standardGeneric(".buildRange"), <environment>)
4: .buildRange(range = range, start = start, end = end, width = width,
       args = list(feature = feature, group = group, id = id, strand =
strand),
       defaults = list(feature = "unknown", group = group, id = id,
           strand = strand, density = 1), chromosome = chromosome)
3: AnnotationTrack(chromosome = "chr6", genome = "hg19", name = "CpG
Islands",
       start = logical(0), end = logical(0))
2: do.call(trackType, args = c(list(chromosome = chromosome, genome =
genome,
       name = name), args))
1: UcscTrack(track = "CpG Islands", chromosome = "chr6", genome = "hg19",
       start = "chromStart", end = "chromEnd", name = "CpG Islands",
       from = 31731740, to = 31736112)

> sessionInfo()
R version 2.15.1 Patched (2012-07-01 r59713)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=C                     LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

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

other attached packages:
[1] Gviz_1.0.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.18.1 Biobase_2.16.0       BiocGenerics_0.2.0
 [4] biomaRt_2.12.0       Biostrings_2.24.1    bitops_1.0-4.1
 [7] BSgenome_1.24.0      DBI_0.2-5            GenomicRanges_1.8.12
[10] IRanges_1.14.4       lattice_0.20-6       RColorBrewer_1.0-5
[13] RCurl_1.91-1         Rsamtools_1.8.5      RSQLite_0.11.1
[16] rtracklayer_1.16.2   stats4_2.15.1        tools_2.15.1
[19] XML_3.9-4            zlibbioc_1.2.0



-- 
Winston Timp
(410)-417-8467
Postdoctoral Fellow
Johns Hopkins Medicine

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