[Bioc-devel] namespace question

[Hervé Pagès]

On 03/31/2016 07:05 AM, Michael Lawrence wrote:
> We should probably deprecate values(). It has long been superseded by
> mcols().

FWIW this is on my long-term list but it can't be done now. values()
was originally (and is still) a RangedData accessor. At some point it
was also made a synonym of elementMetadata() (a.k.a. mcols()) for
Vector derivatives. The goal was to make it easier for package
developers to write code that would operate the same way on GRanges
or RangedData objects. I think easyRNASeq is one of those packages.
Those packages need to be modified to use only GRanges objects
before they can start using mcols() instead of values(). It will
take a long time before we can deprecate values()...

H.

> 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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-- 
Hervé Pagès

Program in Computational Biology
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