[BioC] Error with unique

[Erik Wright]

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?

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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