[Bioc-devel] namespace question
luke-tierney at uiowa.edu
luke-tierney at uiowa.edu
Fri Apr 1 01:00:34 CEST 2016
I don't think you want to separate it from the import. Better to allow
something like
import(foo, exclude=bar)
or
import(foo, exclude=c("bar", "baz"))
This seems reasonably natural and shouldn't be too hard to
implement. (But is has been a while since I've worked on this code).
Best,
luke
On Thu, 31 Mar 2016, Karim Mezhoud wrote:
> I think "From" is needed to specify which package we want to exlude
> functions.
>
> I think excludeFrom (package, function) seems to be intuitive.
>
> thanks,
> Karim
>
>
>
> On Thu, Mar 31, 2016 at 9:54 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
>
>> On 03/31/2016 12:55 PM, Michael Lawrence wrote:
>>
>>> 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.
>>>
>>
>> Fair enough. Not really intuitive that excludeImport uses the same
>> syntax as (but does the opposite of) importFrom though. Maybe having
>> the name of the directive start with "import" would help e.g.
>>
>> importExcept(hash, values) # opposite of importFrom(hash, values)
>>
>> Thanks,
>> H.
>>
>>
>>
>>> 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]]
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>>>>>>
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>>>>>>>>>>>
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>>>>>>>>>>>
>>>>>>>>>>> vEdYoq-VrN42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8
>>>>>>>>>>> CzeHHAAJ5kmgmJxQ&e=
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mai
>>>>>>>>>>
>>>>>>>>>> lman_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY
>>>>>>>>>>
>>>>>>>>>> _w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEd
>>>>>>>>>>
>>>>>>>>>> Yoq-VrN42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeH
>>>>>>>>>> HAAJ5kmgmJxQ&e=
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>
>>>>>>>>
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>>>>>>>>
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>>>>>>>>
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>>>>>>>>
>>>>>>>> N42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmg
>>>>>>>> mJxQ&e=
>>>>>>>>
>>>>>>>>
>>>>>>> [[alternative HTML version deleted]]
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>
>>>>>>>
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>>>>>>>
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>>>>>>>
>>>>>>> PlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-VrN42
>>>>>>>
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>>>>>>> &e=
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>
>>>>>>
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
>>>>>>
>>>>>> _listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
>>>>>>
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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
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>>
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_
>>>>>
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>>>>>
>>>>> hQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-VrN42rfiK5-
>>>>> UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmgmJxQ&e=
>>>>>
>>>>
>>>>
>> --
>> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tierney at uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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