[BioC] Curious error with 'subseq' function from BSgenome (IRanges)

[J.delasHeras at ed.ac.uk]

Quoting Martin Morgan <mtmorgan at fhcrc.org>:

> On 06/04/2010 03:52 AM, J.delasHeras at ed.ac.uk wrote:
>>
>> Hi everyone,
>>
>> I am using the BSgenome package and annotations to retrieve several
>> thousand sequences (22k) corresponding to a promoter microarray.
>>
>> Basically I run a loop through the whole list of chromosome name, start,
>> and stop coordinates, and retrieve each 1Kb sequence using the 'subseq'
>> function.
>>
>> When I run it, I get the following error *sometimes*:
>> Error in get(name, envir = .classTable) :
>>   formal argument "envir" matched by multiple actual arguments
>
> Hi Jose --
>
> This sounds like a bug in R, fixed in the R-2.11.* series, and updating
> your R (and packages, see http://bioconductor.org/docs/install/) should
> fix this. If not, it would be great to hear...
>
> Martin


Hi Martin,

I have the latest R installed as well, I just hadn't installed the  
annotation packages so I used my previous R install for this task.
I'll try again later today with the latest shiniest R/BioC and will  
report back.

Jose


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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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