[Bioc-devel] namespace question
Michael Lawrence
lawrence.michael at gene.com
Fri Apr 1 22:39:36 CEST 2016
Yes, it's arbitrary R code that is evaluated, so paste0() would work.
You're right that it's a big door and could let people do weird
things. Do you foresee a problem with that?
I guess one could have implemented NAMESPACE parsing by evaluating the
code in an environment (inheriting from the base namespace) where
import(), export(), etc, were defined. Maybe there's a good reason why
it was not implemented that way.
On Fri, Apr 1, 2016 at 12:55 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
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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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>>>>>>>>>>>>>
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>>>>>>>>>>>>>
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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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>>>>>>>>>>>
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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
>>>>>>>>>>
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>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>>
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>>>>>>>>>> n_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4Der
>>>>>>>>>>
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>>>>>>>>>> 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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