[BioC] removing packages from the workspace - is this ok?

[Harris A. Jaffee]

This will get you started, but it's probably not the full answer.

? getAnywhere
? ls

For example, ls(2), but note that this contains more than just
functions, e.g. letters in base or IUPAC_CODE_MAP in Biostrings.

On Jun 9, 2011, at 8:12 AM, J.delasHeras at ed.ac.uk wrote:

>
> Hi Herve,
>
> this indeed was the issue I had, which works perfectly well by  
> following Steve's suggestion: simply explicitly renaming objects to  
> ensure one deals with the correct one. The idea of explicitly  
> indicating the package using the double semicolon had escaped me  
> too, so thank you for bringing it up.
>
> Another related matter would be: what happens when two packages use  
> two different functions that are however named identically? I can't  
> think of any right now, but I remember having come across this at  
> some point.
> I imagine that using the same approach (double semicolon to  
> explicitly indicate which package teh function is in) will work.
>
> Is there a simple way to check a function name and return which of  
> the loaded packages have a function with that name? And a list of  
> functions included in a given package?
> This seems to be somewhat basic, but I don't think I've found *one*  
> place to refer to all these issues. If someone can suggest a good  
> place to find this information and better understand all the  
> package/namespace/reference (double semicolon qualifier)  
> nomenclature & structure, I'd be very grateful.
>
> Thank you everyone for their suggestions.
>
> Jose
>
>
> Quoting Hervé Pagès <hpages at fhcrc.org> on Wed, 08 Jun 2011 12:55:20  
> -0700:
>
>> Hi Jose, Steve, Tim,
>>
>> It seems to me that the more general question Jose is asking is how
>> to unambiguously refer to an object when several objects with the  
>> same
>> name are defined in several packages.
>>
>> One solution is to use the "fully qualified name" of the object i.e.
>> to use a <pkgname>:: prefix. For example:
>>
>>   BSgenome.Hsapiens.UCSC.hg18::Hsapiens
>>   BSgenome.Hsapiens.UCSC.hg19::Hsapiens
>>
>> For convenience, this can be combined with Steve's suggested
>> reassignment to shorter names:
>>
>>   hg18 <- BSgenome.Hsapiens.UCSC.hg18::Hsapiens
>>   hg19 <- BSgenome.Hsapiens.UCSC.hg19::Hsapiens
>>
>> By using the "fully qualified name", the result of this reassignment
>> doesn't depend on the order the packages were loaded anymore.
>>
>> Cheers,
>> H.
>>
>>
>> On 11-06-07 02:06 PM, Tim Triche, Jr. wrote:
>>> you're right, it's more of a general solution.  I end up with  
>>> multiple
>>> versions of annotation packages, multiple namespaces' worth of S4  
>>> generics,
>>> etc. floating around and it is a nice swiss army chainsaw (like  
>>> many of
>>> Hadley's packages) with some remaining rough edges.  The ability  
>>> to just
>>> "find a bigger hammer" appeals to me, but a purposeful solution  
>>> is probably
>>> better for the problem at hand.
>>>
>>>
>>> On Tue, Jun 7, 2011 at 12:53 PM, Steve Lianoglou<
>>> mailinglist.honeypot at gmail.com>  wrote:
>>>
>>>> Hi,
>>>>
>>>> On Tue, Jun 7, 2011 at 2:34 PM, Tim Triche,  
>>>> Jr.<tim.triche at gmail.com>
>>>> wrote:
>>>>> One solution to the issue of managing packages in your R
>>>>> namespace/environment is Hadley Wickham's devtools
>>>>> package<https://github.com/hadley/devtools#readme>.
>>>>>  I am surprised more people don't use it for this
>>>>
>>>> I actually tried using that a while ago in order to help make  
>>>> package
>>>> development easier, but:
>>>>
>>>> (1) Isn't that more for being able to work with "source"  
>>>> packages w/o
>>>> having to install them; and
>>>> (2) as an aside, back then it had some problems with S4-isms (which
>>>> may have been fixed by now)
>>>>
>>>> As with most all of Hadley's work -- I think devtools is (will be)
>>>> great, but I don't quite see how that's the right tool for this  
>>>> job,
>>>> though ... ?
>>>>
>>>> -steve
>>>>
>>>> --
>>>> Steve Lianoglou
>>>> Graduate Student: Computational Systems Biology
>>>>  | Memorial Sloan-Kettering Cancer Center
>>>>  | Weill Medical College of Cornell University
>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>>>
>>>
>>>
>>>
>>
>>
>> -- 
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>>
>
>
>
> -- 
> Dr. Jose I. de las Heras                      Email:  
> J.delasHeras at ed.ac.uk
> The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131  
> 6507090
> Institute for Cell & Molecular Biology        Fax:   +44 (0)131  
> 6507360
> Swann Building, Mayfield Road
> University of Edinburgh
> Edinburgh EH9 3JR
> UK
>
>
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
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