[Bioc-devel] namespace question

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Thu Mar 31 21:11:58 CEST 2016


Herve,

That is a very interesting idea and works for me! Thanks!

importPatternFrom(IRanges, "^values$")


Best,

Julie

On 3/31/16 2:51 PM, "Bioc-devel on behalf of Hervé Pagès"
<bioc-devel-bounces at r-project.org on behalf of hpages at fredhutch.org> wrote:

>On 03/30/2016 08:35 PM, Michael Lawrence wrote:
>> That would work, but R is not going to be happy about redundant
>> imports. Interactively, users would balk at symbol qualification.
>>
>> There are two classes of conflict:
>> 1) Same semantics, where a common generic would arbitrate, or one
>> package could depend on the other, and
>> 2) Different semantics, in which case one of the functions should
>> probably be renamed, although that might not be practical or easy to
>> agree upon.
>>
>> When those approaches fail, qualification is the only recourse.
>>
>> I will think about adding an excludeImport() or importAs().
>
>What about having something like an importPatternFrom() directive
>similar to the exportPattern() directive and have these directives
>support some of the grep() toggles like 'ignore.case', 'fixed',
>'invert' etc... ?
>
>Then Julie could just do:
>
>importPatternFrom(hash, "^values$", invert=TRUE)
>
>H.
>
>>
>>
>> On Wed, Mar 30, 2016 at 8:20 PM, Robert M. Flight <rflight79 at gmail.com>
>>wrote:
>>> In the cases of having conflicting names, is it not appropriate then
>>>to use
>>> the "package::function" form for calling a particular function?
>>>
>>> On Wed, Mar 30, 2016 at 11:14 PM Michael Lawrence
>>><lawrence.michael at gene.com>
>>> wrote:
>>>
>>>> I can't find the hash function in IRanges. Are you sure it has one?
>>>>
>>>> On Wed, Mar 30, 2016 at 8:07 PM, Zhu, Lihua (Julie)
>>>> <Julie.Zhu at umassmed.edu> wrote:
>>>>> Michael,
>>>>>
>>>>> I have the same user case as Kasper. Another example is that both
>>>>>IRanges
>>>>> and hash packages have hash. I need to use the hash from the hash
>>>>>package
>>>>> instead of the one from IRanges.
>>>>>
>>>>> Best,
>>>>>
>>>>> Julie
>>>>>
>>>>> On Mar 30, 2016, at 7:57 PM, Kasper Daniel Hansen
>>>>> <kasperdanielhansen at gmail.com> wrote:
>>>>>
>>>>> My usecase is when I import() two packages who has a conflict in a
>>>>>name.
>>>>> For example, both Biobase and matrixStats has both anyMissing and
>>>>> rowMedians. I am happy to get all of these two packages, but I need
>>>>>to
>>>>> resolve the conflict.  Since I want to keep the ones from
>>>>>matrixStats I
>>>> know
>>>>> need to figure out how to import Biobase selectively.  Which I can,
>>>>>using
>>>>> the tools from codetoolsBioC, but I would also be happy with an
>>>>> importFromExcept(), which would make my life much easier.
>>>>>
>>>>> Best,
>>>>> Kasper
>>>>>
>>>>> On Wed, Mar 30, 2016 at 4:47 PM, Michael Lawrence
>>>>> <lawrence.michael at gene.com> wrote:
>>>>>>
>>>>>> I'm curious about which symbols you wouldn't want to import, and
>>>>>>why.
>>>>>>
>>>>>> On Wed, Mar 30, 2016 at 12:19 PM, Zhu, Lihua (Julie)
>>>>>> <Julie.Zhu at umassmed.edu> wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> Is there a function to import all the exported objects from a
>>>>>>>package
>>>>>>> except a few named ones in NAMESPACE file?
>>>>>>>
>>>>>>> For example, I would like to import all the functions in S4Vectors
>>>>>>> except fold. Is there a way to  specify this without listing all
>>>>>>>other
>>>>>>> functions using importFrom?
>>>>>>>
>>>>>>> Many thanks for your help!
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Julie
>>>>>>>
>>>>>>> ********************************************
>>>>>>> Lihua Julie Zhu, Ph.D
>>>>>>> Research Professor
>>>>>>> Department of Molecular, Cell and Cancer Biology (MCCB)
>>>>>>> Head of MCCB Bioinformatics Core
>>>>>>> Program in Molecular Medicine
>>>>>>> Program in Bioinformatics and Integrative Biology
>>>>>>> University of Massachusetts Medical School
>>>>>>> 364 Plantation Street, Room 613
>>>>>>> Worcester, MA 01605
>>>>>>> 508-856-5256 phone
>>>>>>> (508) 856 5460 fax
>>>>>>>
>>>>>>>
>>>> 
>>>>http://profiles.umassmed.edu/profiles/ProfileDetails.aspx?From=SE&Perso
>>>>n=1134
>>>>>>>
>>>>>>>
>>>>>>>          [[alternative HTML version deleted]]
>>>>>>>
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>>>>
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>>
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>
>-- 
>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 fredhutch.org
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319
>
>_______________________________________________
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