[Bioc-sig-seq] BSGenome: Intermittent failure in getSeq, matchPattern and findOverlaps

[Seth Falcon]

Hi Aaron,

On 3/8/10 1:30 AM, Aaron Statham wrote:
> For the last few days I've been coming across a show-stopping bug when
> performing sequence analysis using BSgenome - my code fails either in
> getSeq, matchPattern or findOverlaps in a completely intermittent way,
> with the only consistent error message being inside either a get() or
> assign() call:
>
> "formal argument "envir" matched by multiple actual arguments"

Thanks for reporting this and providing a reproducible case.  I can get 
the same error using your script and hope to be able to track down the 
root cause and provide a fix.

> Any suggestions/workarounds? Or would this be better posted to the
> R-devel list?

Give us a couple days to track this down.  Not sure what to suggest for 
workarounds other than adding some error checking and try repeating the 
computation when it fails.

+ seth

-- 
Seth Falcon
Bioconductor Core Team | FHCRC