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

Thu Jun 9 18:00:22 CEST 2011

thank you, I was not aware of ls() being able to return these data.

Jose

Quoting "Harris A. Jaffee" <hj at jhu.edu> on Thu, 9 Jun 2011 09:15:22 -0400:

> 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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>
>
>

-- 
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.