[Bioc-devel] namespace question
Hervé Pagès
hpages at fredhutch.org
Fri Apr 1 21:55:30 CEST 2016
On 03/31/2016 04:07 PM, Michael Lawrence wrote:
> I agree. The importExcept idea also works that way: importExcept(foo, bar, baz)
>
> But import(foo, except=c(bar, baz)) reads better.
mmh... so R expressions with calls to base functions like base::c() are
making their way in the NAMESPACE file. That's opening a big door. Does
that mean that we'll be able to do things like:
import(foo, except=paste0("bar", 1:10))
Or maybe c(bar, baz) in your above example is just an arbitrary syntax
that just happens to look like an R expression but won't be evaluated
as such?
H.
>
>
> 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
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ilman_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeR
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> jY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=Rxzbh
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> vEdYoq-VrN42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8
>>>>>>>>>>>>> CzeHHAAJ5kmgmJxQ&e=
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>>>
>>>>>>>>>>>>
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>>>>>>>>>>>>
>>>>>>>>>>>> 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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>>>>>>>>>> an_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D
>>>>>>>>>>
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>>>>>>>>>> erPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-Vr
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> N42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmg
>>>>>>>>>> mJxQ&e=
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> [[alternative HTML version deleted]]
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailma
>>>>>>>>>
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>>>>>>>>> n_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4Der
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> PlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-VrN42
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmgmJxQ
>>>>>>>>> &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
>>>>>>>>
>>>>>>>>
>>>>>>>> OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-VrN42rfi
>>>>>>>>
>>>>>>>>
>>>>>>>> K5-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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_
>>>>>>>
>>>>>>>
>>>>>>> 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
--
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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