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

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Fri Jun 4 13:35:41 CEST 2010

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.


Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6507095
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