I have run into a different problem with the devel version of Gviz:

If I try to plot a GeneRegionTrack derived from UCSC at a location which
overlaps a gene, but none of its exons, it fails, complaining as shown
below.  If I extend the plot range to overlap with an exon, (AKA
from=122426300), it works.

Is there a workaround for this/am I making an obvious error?  I assume that
it is exploding because it expects at least one exon in the plotted region.
 Even if I set the collapseTranscripts flag, it still fails, probably
because that step is after finding exons within region.

traceback and sessionInfo below

Thanks,

Winston

> library(Gviz)
Loading required package: grid
> genetrack=UcscTrack(track="RefSeq Genes", table="refGene",
trackType="GeneRegionTrack",chromosome="chr5", genome="hg19",
rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2",
transcript="name", strand="strand", name="RefSeq Genes", feature="name2",
showId=T, from=122428653, to=122432628)
> plotTracks(genetrack, from=122428653, to=122432628)
Error in unit(rep(1, n), "strwidth", data = data) :
  'x' and 'units' must have length > 0
> traceback()
12: stop("'x' and 'units' must have length > 0")
11: unit(rep(1, n), "strwidth", data = data)
10: stringWidth(identifier(GdObject, add.space = TRUE))
9: is.unit(x)
8: convertUnit(x, unitTo, "x", "dimension", "x", "dimension", valueOnly =
valueOnly)
7: convertWidth(stringWidth(identifier(GdObject, add.space = TRUE)),
       "native")
6: .local(GdObject, ...)
5: FUN(X[[1L]], ...)
4: FUN(X[[1L]], ...)
3: lapply(trackList, setStacks, from = ranges["from"], to = ranges["to"])
2: lapply(trackList, setStacks, from = ranges["from"], to = ranges["to"])
1: plotTracks(genetrack, from = 122428653, to = 122432628)
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

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

other attached packages:
[1] Gviz_1.1.12

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.19.29  BSgenome_1.25.6        Biobase_2.17.6
 [4] BiocGenerics_0.3.1     Biostrings_2.25.12     DBI_0.2-5
 [7] GenomicFeatures_1.9.31 GenomicRanges_1.9.53   IRanges_1.15.40
[10] RColorBrewer_1.0-5     RCurl_1.91-1           RSQLite_0.11.1
[13] Rsamtools_1.9.28       XML_3.9-4              biomaRt_2.13.2
[16] bitops_1.0-4.1         lattice_0.20-6         rtracklayer_1.17.19
[19] stats4_2.15.1          tools_2.15.1           zlibbioc_1.3.0

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

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