[BioC] Error with unique

[Erik Wright]

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.
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> 
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