[Bioc-devel] namespace question
Michael Lawrence
lawrence.michael at gene.com
Fri Apr 1 01:07:52 CEST 2016
I agree. The importExcept idea also works that way: importExcept(foo, bar, baz)
But import(foo, except=c(bar, baz)) reads better.
On Thu, Mar 31, 2016 at 4:00 PM, <luke-tierney at uiowa.edu> wrote:
> 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
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_ma
>>>>>>>>>>>>
>>>>>>>>>>>>
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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
>>>>>>>>>>>
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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Yoq-VrN42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeH
>>>>>>>>>>> HAAJ5kmgmJxQ&e=
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>
>>>>>>>>>
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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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>>>>>>>>
>>>>>>>>
>>>>>>>> rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmgmJxQ
>>>>>>>> &e=
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>
>>>>>>>
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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
>>>>>>
>>>>>>
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>>>>>>
>>>>>>
>>>>>> listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOm
>>>>>>
>>>>>>
>>>>>> 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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