[Bioc-devel] namespace question

[Kasper Daniel Hansen]

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 It has long been superseded by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]]
> >>>> >
> >>>> > _______________________________________________
> >>>> > Bioc-devel at r-project.org mailing list
> >>>> >
> >>>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailma
>
> >>>>n_listinfo_bioc-2Ddevel&d=BQIBaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4Der
>
> >>>>PlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=K-j995DBKSpPEMWrL
>
> >>>>Wklcv4lQEiFC7wPFwn1ssv9dtg&s=fijAc5Y3bbV4ei4vYEx_SXy9kDcQ8vNUPOrE0cq1eZk
> >>>>&e=
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-devel at r-project.org mailing list
> >>>>
> >>>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailma
>
> >>>>n_listinfo_bioc-2Ddevel&d=BQIBaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4Der
>
> >>>>PlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=K-j995DBKSpPEMWrL
>
> >>>>Wklcv4lQEiFC7wPFwn1ssv9dtg&s=fijAc5Y3bbV4ei4vYEx_SXy9kDcQ8vNUPOrE0cq1eZk
> >>>>&e=
> >>>
> >>>
> >
>

	[[alternative HTML version deleted]]