Please try 1.10.6, when it comes out.

Thanks,
Michael

On Wed, Dec 8, 2010 at 2:00 PM, Meier, Samuel <srm@stowers.org> wrote:

> Hello,
>
> I am trying to use the liftOver function from the rtracklayer package, but
> I receive the following error message when attempting to import the chain
> file downloaded from UCSC.
>
> > import.chain("dm3ToDp3.over.chain")
> Error in getClass("Alignment") : "Alignment" is not a defined class
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] rtracklayer_1.10.3
>  [2] RCurl_1.4-3
>  [3] bitops_1.0-4.1
>  [4] BSgenome.Dyakuba.UCSC.droYak2_1.0.0
>  [5] BSgenome.Dsimulans.UCSC.droSim1_1.0.0
>  [6] BSgenome.Dpseudoobscura.UCSC.dp3_1.0.0
>  [7] BSgenome.Derecta.UCSC.droEre1_1.0.0
>  [8] BSgenome.Dananassae.UCSC.droAna2_1.0.0
>  [9] BSgenome.Dmelanogaster.UCSC.dm3_1.3.16
> [10] BSgenome_1.18.0
> [11] Biostrings_2.18.0
> [12] GenomicRanges_1.2.1
> [13] IRanges_1.8.2
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.10.0 XML_3.2-0      tools_2.12.0
>
> Thanks,
> Sam Meier
>
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