[Bioc-devel] namespace question

I agree. The importExcept idea also works that way: importExcept(foo, bar, baz)

But import(foo, except=c(bar, baz)) reads better.

On Thu, Mar 31, 2016 at 4:00 PM,  <luke-tierney at uiowa.edu> wrote:

I don't think you want to separate it from the import. Better to allow
something like

import(foo, exclude=bar)

or

import(foo, exclude=c("bar", "baz"))

This seems reasonably natural and shouldn't be too hard to
implement. (But is has been a while since I've worked on this code).

Best,

luke


On Thu, 31 Mar 2016, Karim Mezhoud wrote:

I think "From" is needed to specify which package we want to exlude
functions.

I think  excludeFrom (package, function)  seems to be intuitive.

thanks,
Karim



On Thu, Mar 31, 2016 at 9:54 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:

On 03/31/2016 12:55 PM, Michael Lawrence wrote:

Probably should just stick to exact symbols for now. If there is a
case where a pattern is actually useful, rather than just an
obfuscation, we can extend the feature set.

Fair enough. Not really intuitive that excludeImport uses the same
syntax as (but does the opposite of) importFrom though. Maybe having
the name of the directive start with "import" would help e.g.

importExcept(hash, values)  # opposite of importFrom(hash, values)

Thanks,
H.

On Thu, Mar 31, 2016 at 12:11 PM, Zhu, Lihua (Julie)
<Julie.Zhu at umassmed.edu> wrote:

Herve,

That is a very interesting idea and works for me! Thanks!

importPatternFrom(IRanges, "^values$")


Best,

Julie

On 3/31/16 2:51 PM, "Bioc-devel on behalf of Herv? Pag?s"
<bioc-devel-bounces at r-project.org on behalf of hpages at fredhutch.org>
wrote:

On 03/30/2016 08:35 PM, Michael Lawrence wrote:

That would work, but R is not going to be happy about redundant
imports. Interactively, users would balk at symbol qualification.

There are two classes of conflict:
1) Same semantics, where a common generic would arbitrate, or one
package could depend on the other, and
2) Different semantics, in which case one of the functions should
probably be renamed, although that might not be practical or easy to
agree upon.

When those approaches fail, qualification is the only recourse.

I will think about adding an excludeImport() or importAs().

What about having something like an importPatternFrom() directive
similar to the exportPattern() directive and have these directives
support some of the grep() toggles like 'ignore.case', 'fixed',
'invert' etc... ?

Then Julie could just do:

importPatternFrom(hash, "^values$", invert=TRUE)

H.

On Wed, Mar 30, 2016 at 8:20 PM, Robert M. Flight
<rflight79 at gmail.com

wrote:

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&Perso
n=1134

           [[alternative HTML version deleted]]

           [[alternative HTML version deleted]]

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

         [[alternative HTML version deleted]]

--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu