[Bioc-devel] namespace question

[Michael Lawrence]

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 It has long been superseded by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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>>>
>