[Bioc-devel] namespace question

Thu Mar 31 21:55:09 CEST 2016

Probably should just stick to exact symbols for now. If there is a
case where a pattern is actually useful, rather than just an
obfuscation, we can extend the feature set.

On Thu, Mar 31, 2016 at 12:11 PM, Zhu, Lihua (Julie)
<Julie.Zhu at umassmed.edu> wrote:
> 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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>>
>>--
>>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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>