I have been perplexed by this and can't seem to get any traction debugging
it.
A quick Google search didn't turn up anything useful.  I've had liftOver()
work properly in the past, but not this time...

# example
> CpH.fwd = with(CpH, GRanges(chr, IRanges(end=site,width=50),
strand=CpH.strand, names=rownames(CpH)))
> CpH.fwd
GRanges with 3091 ranges and 1 elementMetadata value:
         seqnames               ranges strand   |           names
            <Rle>            <IRanges>  <Rle>   |     <character>
     [1]     chrX [ 7556494,  7556543]      -   |   ch.X.7566543R
     [2]     chrX [10104084, 10104133]      -   |    ch.X.147603R
     [3]     chrX [12813493, 12813542]      -   |    ch.X.188238R
# ...
> hg18hg19 = import.chain('hg18ToHg19.over.chain')
> liftOver(CpH.fwd, hg18hg19)
Error in unique.default(x) : unique() applies only to vectors

Anyone seen this before?  Is it a sign that something is amiss or is it
perhaps a bug?

> sessionInfo()
R Under development (unstable) (2011-10-13 r57229)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] rtracklayer_1.13.19
 [2] RCurl_1.6-10
 [3] bitops_1.0-4.1
 [4] BSgenome.Hsapiens.UCSC.hg19_1.3.17
 [5] BSgenome_1.21.7
 [6] Biostrings_2.21.11
 [7] GenomicRanges_1.5.51
 [8] IRanges_1.11.31
 [9] IlluminaHumanMethylation450kprobe_1.9.12
[10] AnnotationDbi_1.15.38
[11] Biobase_2.13.11
[12] BiocInstaller_1.1.28
[13] gtools_2.6.2

loaded via a namespace (and not attached):
[1] DBI_0.2-5      RSQLite_0.10.0 tools_2.15.0   XML_3.4-3
 zlibbioc_0.1.8


-- 
If people do not believe that mathematics is simple,
it is only because they do not realize how complicated life is.John von
Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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