Thanks for this report. Not sure what was happening there. I have been
significantly refactoring rtracklayer (internally) and this error no longer
occurs. The new rtracklayer is in the process of gaining a full test suite,
and this has been added as a regression test.

I could try to fix this in the release, but it looks like you have a
reasonable workaround.

Michael

On Thu, Jan 19, 2012 at 10:53 AM, Cook, Malcolm <MEC@stowers.org> wrote:

> I find that
>
>        x<-import (pipe("head my.bed"),'bed')
>
> succeeds, thank you very much ;)
>
> whereas both of the following
>
>        x<-import.bed(pipe("head my.bed"))
>
>        x<-import.bed(pipe("head my.bed"),'base',TRUE)
>
> hang, never returning and using CPU ;(
>
> Is there a difference I am not appreciating, or is this a BUG?
>
> Thanks,
>
> Malcolm Cook
> Stowers Institute for Medical Research
>
>
> > sessionInfo()
> R version 2.14.0 (2011-10-31)
> 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_1.14.4 RCurl_1.9-4        bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.22.0     Biostrings_2.22.0   GenomicRanges_1.6.4
> [4] IRanges_1.12.5      XML_3.6-2           tools_2.14.0
> [7] zlibbioc_1.0.0
> >
>
>

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