[Bioc-devel] namespace question
Yes, it's arbitrary R code that is evaluated, so paste0() would work. You're right that it's a big door and could let people do weird things. Do you foresee a problem with that? I guess one could have implemented NAMESPACE parsing by evaluating the code in an environment (inheriting from the base namespace) where import(), export(), etc, were defined. Maybe there's a good reason why it was not implemented that way.
On Fri, Apr 1, 2016 at 12:55 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:
On 03/31/2016 04:07 PM, Michael Lawrence wrote:
I agree. The importExcept idea also works that way: importExcept(foo, bar, baz) But import(foo, except=c(bar, baz)) reads better.
mmh... so R expressions with calls to base functions like base::c() are
making their way in the NAMESPACE file. That's opening a big door. Does
that mean that we'll be able to do things like:
import(foo, except=paste0("bar", 1:10))
Or maybe c(bar, baz) in your above example is just an arbitrary syntax
that just happens to look like an R expression but won't be evaluated
as such?
H.
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
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-- 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
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-- 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
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-- 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