[BioC] Error with unique

[Martin Morgan]

On 04/05/2010 07:23 PM, Erik Wright wrote:
> Hi Sean,
> 
> Here is a simple function that creates the problem:
> doUnique <- function(myDNAStringSet) {
> 	myDNAStringSet <- unique(myDNAStringSet)
> }
> 
> Here is the output in the R Console:
>> doUnique(myDNAStringSet)
> Error in unique.default(myDNAStringSet) : 
>   unique() applies only to vectors

Likely it is a NAMESPACE issue. Either doUnique is defined in
GoneFISHing but the NAMESPACE of GoneFISHing does not have

  importFrom(Biostrings, unique)

or GoneFISHing defines and/or exports its own unique that masks the one
exported by  Biostrings. If these were packages written by people who
didn't talk with one another then you could specify

  Biostrings::unique(myDNAStringSet)

but likely the solution is to develop an appropriate NAMESPACE in
GoneFISHing. The codetoolsBioC package at

  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC

accessible using svn, see

  http://wiki.fhcrc.org/bioc/SvnHowTo

might be helpful.

Martin

>> sessionInfo()
> R version 2.10.1 (2009-12-14) 
> i386-apple-darwin9.8.0 
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods  
> [7] base     
> 
> other attached packages:
> [1] GoneFISHing_1.0.5  RSQLite_0.8-3      DBI_0.2-5         
> [4] Biostrings_2.14.12 IRanges_1.4.11    
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.6.1
> 
> Thanks again!,
> Erik
> 
> 
> On Apr 5, 2010, at 8:55 PM, Sean Davis wrote:
> 
>> On Mon, Apr 5, 2010 at 9:51 PM, Erik Wright <eswright at wisc.edu> wrote:
>>> Hi all,
>>>
>>> I am using the unique(x) function with a DNAStringSet in one of my own functions.  Recently my function has started returning an error, and I am not sure what changed.  The same line of code works fine in the R Console, just not in my function.  I am using the function as:
>>>
>>> myDNAStringSet <- unique(myDNAStringSet)
>>>
>>> When I run my function the error returned is:
>>>
>>> Error in unique.default(myDNAStringSet) :
>>>  unique() applies only to vectors
>>>
>>> I am guessing that the R is trying to apply the unique function in the base package to the DNAStringSet rather than using the unique function in the Biostrings package.  Is there a solution to this?
>>>
>>
>> Hi, Erik.  A reproducible example and sessionInfo() would be helpful.
>>
>> Sean
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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