[BioC] Error with unique

[Martin Morgan]

On 04/06/2010 04:43 AM, Erik Wright wrote:
> Hi Martin,
> 
> When I tried using "Biostrings::unique(myDNAStringSet)", I got this error instead:
> Error: 'unique' is not an exported object from 'namespace:Biostrings'
> 
> Any ideas?

My bad, sorry. IRanges::unique(). The generic is defined in IRanges, the
method for DNAStringSet attached to that generic.

Martin

> 
> Thanks!,
> Erik
> 
> 
> On Apr 6, 2010, at 6:37 AM, Erik Wright wrote:
> 
>> Hi Martin,
>>
>> In Writing R Extensions it says that "the import directive imports all exported variables from the specified package(s).":
>>
>> http://cran.r-project.org/doc/manuals/R-exts.html#Specifying-imports-and-exports
>>
>> Since my NAMESPACE file already says import(Biostrings), do I also need to use importFrom(Biostrings, x, y, z) for each x, y, z function I want to use?
>>
>> Also, where do I get the username/password that I need to access svn?
>>
>> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor Subversion Repository
>> Password for 'me': 
>> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor Subversion Repository
>> Username: svn: OPTIONS of 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC': authorization failed: Could not authenticate to server: rejected Basic challenge (https://hedgehog.fhcrc.org)
>>
>> Thanks!,
>> Erik
>>
>>
>> On Apr 5, 2010, at 10:01 PM, Martin Morgan wrote:
>>
>>> 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
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>
>> _______________________________________________
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> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793