[BioC] Error with unique

[Martin Morgan]

On 04/06/2010 06:17 AM, Martin Morgan wrote:
> 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.

maybe connecting the dots a little with your other email. Perhaps you
are missing importFrom(IRanges, unique)? Martin

>>
>> 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
>>>> mailing list Bioconductor at stat.math.ethz.ch 
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
>>>> archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>>
>>>>


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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