Just to follow up, I've been able to get it to work without any errors after
shutting down various X11 windows.  At one point, I got an X11 fatal IO
error: please save work and shut down R.

So, I don't have a great explanation on my end.

Andrew

2010/3/4 Andrew Yee <yee@post.harvard.edu>

> Thanks for checking.  Note, I'm accessing Linux through putty on my Windows
> machine.  I've also encountered this problem when I'm using Linux directly.
>
>
> Here's my sessionInfo()
>
>  R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> 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=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       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 utils     datasets  methods   base
>
> other attached packages:
> [1] IRanges_1.4.11
>
>
>
> 2010/3/4 Hervé Pagès <hpages@fhcrc.org>
>
> Hi Andrew,
>>
>> I'm running BioC 2.5 + R 2.10.1 on a Linux system too but I can't
>> reproduce this (I'm not even asked to choose between base::sort
>> and IRanges::sort).
>>
>> Please provide the output of sessionInfo() that you get just after
>> a fresh R start immediately followed by library(IRanges).
>>
>> Thanks,
>> H.
>>
>>
>> Andrew Yee wrote:
>>
>>> I'm not sure where to begin with this problem, but here I go.  I'm
>>> running
>>> this on a Linux system using R 2.10.1
>>>
>>> I've installed the IRanges package.  However, when I enter help(sort), it
>>> shows that the topic 'sort' was found both in the IRanges and the base
>>> package.  However, it ultimately returns an error message,
>>>
>>> Error in structure(.External("dotTclObjv", objv, PACKAGE="tcltk"), class
>>> =
>>> "tclObj") :
>>> [tcl] grab failed: window not viewable.
>>>
>>> Am I missing something obvious?
>>>
>>> Thanks,
>>> Andrew
>>>
>>>        [[alternative HTML version deleted]]
>>>
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>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M2-B876
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages@fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>
>

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