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 <rfligh...@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.mich...@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....@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
<kasperdanielhan...@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.mich...@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....@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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