[Bioc-devel] namespace question

[Michael Lawrence]

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().


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&Person=1134
>> >> >
>> >> >
>> >> >         [[alternative HTML version deleted]]
>> >> >
>> >> > _______________________________________________
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>> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >> _______________________________________________
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>> >
>> >
>>
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