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[Bioc-devel] namespace question

Robert M. Flight

Wed, Mar 30, 2016 8:20 PM

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


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Thread (25 messages)

Zhu, Lihua (Julie) namespace question Mar 30 Kasper Daniel Hansen namespace question Mar 30 Zhu, Lihua (Julie) namespace question Mar 30 Michael Lawrence namespace question Mar 30 Kasper Daniel Hansen namespace question Mar 30 Michael Lawrence namespace question Mar 30 Kasper Daniel Hansen namespace question Mar 30 Zhu, Lihua (Julie) namespace question Mar 30 Michael Lawrence namespace question Mar 30 Robert M. Flight namespace question Mar 30 Michael Lawrence namespace question Mar 30 Zhu, Lihua (Julie) namespace question Mar 31 Michael Lawrence namespace question Mar 31 Kasper Daniel Hansen namespace question Mar 31 Zhu, Lihua (Julie) namespace question Mar 31 Michael Lawrence namespace question Mar 31 Hervé Pagès namespace question Mar 31 Michael Lawrence namespace question Mar 31 Hervé Pagès namespace question Mar 31 Zhu, Lihua (Julie) namespace question Mar 31 Michael Lawrence namespace question Mar 31 Hervé Pagès namespace question Mar 31 Karim Mezhoud namespace question Mar 31 Luke Tierney namespace question Mar 31 Michael Lawrence namespace question Mar 31