This issue has been reported before. The resolution was that there are odd
things going on in the methods package. Pretty sure we reported this to
John.

Thanks,
Michael

On Fri, Jun 10, 2011 at 12:56 PM, Cook, Malcolm <MEC@stowers.org> wrote:

> Michael & Robert,
>
> If I load the graph package prior to rtracklayer, import.bed generates an
> error and fails.  It otherwise succeeds if I don't load the graph package.
>
> It happens both with rtracklayer from svn and production.
>
> Look:
>
> In a fresh session:
>
> > library(graph)
> > library(rtracklayer)
> Loading required package: RCurl
> Loading required package: bitops
> > b <- import.bed('my.bed')
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "import.ucsc", for
> signature "file"
> > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.13.3 RCurl_1.5-0        bitops_1.0-4.1     graph_1.30.0
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.20.0     Biostrings_2.20.1   GenomicRanges_1.4.6
> [4] IRanges_1.10.4      XML_3.4-0           tools_2.13.0
> >
>
>
>
>

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