[Bioc-devel] namespace question

[Michael Lawrence]

You might also consider whether you really need the hash package. It
seems like a pretty lightweight wrapper around environments.

On Thu, Mar 31, 2016 at 7:16 AM, Zhu, Lihua (Julie)
<Julie.Zhu at umassmed.edu> wrote:
> Thanks Kasper! Importing Iranges piecewise is difficult.
>
> Michael, I did use importFrom(hash, …)
>
> importFrom(hash, values, hash)
>
> Also, this is just an example. Thanks for willing to add a function similar
> to importFromExcept()
>
> Best,
>
> Julie
>
>
> From: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
> Date: Thursday, March 31, 2016 9:09 AM
> To: Michael Lawrence <lawrence.michael at gene.com>
> Cc: Lihua Julie Zhu <julie.zhu at umassmed.edu>, "bioc-devel at r-project.org"
> <bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] namespace question
>
> Of course, that depends on whether Julie actually uses hash::values or this
> is just trying to avoid a conflict.  Importing IRanges piecewise is ...
> probably difficult.
>
> Best,
> Kasper
>
> On Thu, Mar 31, 2016 at 10:05 AM, Michael Lawrence
> <lawrence.michael at gene.com> wrote:
>>
>> We should probably deprecate values(). It has long been superseded by
>> mcols(). But for now, it would seem pragmatic to importFrom(hash, ...)
>> since it has so few functions.
>>
>> On Thu, Mar 31, 2016 at 6:54 AM, Zhu, Lihua (Julie)
>> <Julie.Zhu at umassmed.edu> wrote:
>> > Sorry. I meant values.
>> >
>> > replacing previous import ŒIRanges::values¹ by Œhash::values¹ when
>> > loading
>> > ŒCRISPRseek¹
>> >
>> > Best,
>> >
>> > Julie
>> >
>> >
>> > On 3/30/16 11:13 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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>> >>>> >
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