[BioC] Error with unique

[Martin Morgan]

On 04/06/2010 04:37 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?

import() is sufficient. IMHO import() defeats the developer-side purpose
of carefully controlling what functions the package sees.

> 
> Also, where do I get the username/password that I need to access
> svn?

username: readonly
password: readonly

(they're on the wiki page, but made more prominent now).

Martin
> 
> 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
>>> 
>>> _______________________________________________ Bioconductor
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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
> 


-- 
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