Displaying 20 results from an estimated 7000 matches similar to: "format: different S4 behavior in a package"
2012 Dec 08
1
namespace S3 and S4 generic imports cannot both be satisfied:
PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods indicates
that one should
setGeneric("unique")
setClass("A")
unique.A <- function(x, incomparables=FALSE, ...) {}
setMethod(unique, "A", unique.A)
Both S3 and S4 methods need to be exported in the NAMESPACE
import(methods)
S3method(unique, A)
2010 May 29
3
S4 dispatch for .DollarNames (utils)
Hello,
I'm trying to make .DollarNames generic and implement a method for it in
a package. .DollarNames is the function that is now called to get
completion possibilities.
My R code looks like this:
setGeneric( ".DollarNames" )
setClass("track",
representation(x="numeric", y="numeric"))
## A class extending the previous, adding one more
2009 Jan 13
2
particulars of importing/loading libraries
Dear List:
Sorry for posting maybe a trivial question, but I have a basic
understanding problem. If I have say pack1 and pack2, two R packages,
and pack2 depends on and imports pack1 fully (as in the code below), is
there a way to make all the functionality of pack1 available for the
global and other environments (not only for the functions called from
withing pack2) by loading pack2 only? I
2013 Mar 13
1
S4 generic not exported correctly / incorrect dispatch?
In this post
https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html
a package author reports that S4 dispatch fails. I can reproduce this with a
PkgA (attached; 'intervals' is a relatively light-weight CRAN package) that has
DESCRIPTION with
Depends: intervals
Imports: graphics
NAMESPACE:
importFrom(graphics, "plot")
export("plot")
2004 Jan 08
3
S3, S4, namespace
I have encountered an issue which I have been unable to resolve, involving
an S3 generic (print) being declared S4 generic in a package, and the method
being exported. This all works fine - the problem occurs when I try to
import the method to another package.
Here is the bit that works fine. -------------
#the .r file for package bar
2015 May 10
2
S4 method dispatch sometimes leads to incorrect when object loaded from file?
Loading an S4 object from a file without first loading the library sometimes (?,
the example below and actual example involves a virtual base class and the show
generic) leads to incorrect dispatch (to the base class method).
The attached package reproduces the problem. It has
setClass("A")
setClass("B", contains="A")
setMethod("show", "A",
2011 Dec 15
1
R CMD check fails to warn about undocumented classes and methods
In
> R.version.string
[1] "R Under development (unstable) (2011-12-15 r57901)"
PkgA promotes 'unique' to a generic and exports that
DESCRIPTION:
Imports: methods
R/f.R:
setGeneric("unique")
NAMESPACE:
export(unique)
and PkgB creates and exports a method on unique
DESCRIPTION
Imports: methods, PkgA
R/f.R:
setClass("B",
2012 Feb 26
1
improved error message when existing implicit S4 generic is not imported?
pkgA's NAMESPACE has
importFrom(graphics, plot)
exportClasses("A")
exportMethods("plot")
R/foo.R has
setClass("A")
setMethod("plot", "A", function(x, y, ...) {})
During R CMD INSTALL pkgA_1.0.tar.gz we are told
** preparing package for lazy loading
Creating a generic function for 'plot' from package
2011 Dec 15
1
S4 NAMESPACE method imports and exports do not include (promoted?) generics
In
> R.version.string
[1] "R Under development (unstable) (2011-12-15 r57901)"
section 1.6.6 of 'Writing R Extensions' says
Note that exporting methods on a generic in the namespace will
also export the generic, and exporting a generic in the
namespace will also export its methods.
and
Note that importMethodsFrom will also import any generics defined in
2010 Nov 10
1
S4 package warning
Hello everyone. R-2.12.0, suse linux 11.3.
I am debugging a package that uses S4 methods
and R CMD check gives the following warning:
> Warning in methods::findMethods(g, env) :
> non-generic function 'mdm' given to findMethods()
> See the information on DESCRIPTION files in the chapter 'Creating R
> packages' of the 'Writing R Extensions' manual.
I
2015 May 12
1
S4 method dispatch sometimes leads to incorrect when object loaded from file?
>>>>> Martin Morgan <mtmorgan at fredhutch.org>
>>>>> on Mon, 11 May 2015 10:18:07 -0700 writes:
> On 05/10/2015 08:19 AM, Martin Morgan wrote:
>> Loading an S4 object from a file without first loading the library sometimes (?,
>> the example below and actual example involves a virtual base class and the show
>> generic)
2009 Aug 17
2
S4 Generics and NAMESPACE : justified warning ?
Dear list,
It seems that a package (pkgB) using another package (pkgA) with S4
generics formed by taking existing functions (for example 'plot') must
not import the existing functions ('plot') in its namespace to avoid
the warning "replacing previous import: plot".
Suppose we use the simple 'import' directive in the name space of
pkgB.
pkgA and pkgB files would
2011 Aug 23
1
Implementing a "plugin" paradigm with R methods
Dear list,
I was wondering how to best implement some sort of a "plugin" paradigm
using R methods and the dispatcher:
Say we have a function/method ('foo') that does something useful, but
that should be open for extension in ONE specific area by OTHERS using
my package. Of course they could go ahead and write a whole new 'foo'
method including the features they'd
2013 Feb 14
4
2 setGeneric's, same name, different method signatures
hi. below is a small test case (hopefully minimal, though i'm still a
bit confused about initializers).
i would have guessed (and maybe i still would have been right) that one
could re-use the name of a generic function for functions with different
numbers of arguments. in the case below, class A's bB() queries the
status of a single A object, so bB(A) (where here "A" is an
2007 Apr 19
2
setClass inside a function
Hello,
I would like to create a function that gets passed a class name and then calls setClass, and a few other functions, inside. I have done this in the past with setmethod, creating accessors for all slots in a set of S4 classes. But setClass is choking when my function is called isnide a package, telling about an error in exists(cname, where). I assume this to be a problem with the
2012 Apr 12
1
R-2.15.0 and Exporting Methods Converted To S4 Generic
Late to the show on this release, unfortunately.
One of our production packages no longer builds under R-2.15.0
with the following message.
** testing if installed package can be loaded
Error: Function found when exporting methods from the namespace
'SuperCurve' which is not S4 generic: 'image'
Possibly relevant clues follow:
## From R/AllGenerics.R
if
2020 Feb 18
2
Possible Regression in setClassUnion between 3.5.0 and 3.6.0
I am trying to create a class union of class unions to facilitate method
dispatch. When I execute code in the global environment, everything acts as
expected, however when I put the same code in the context of a package,
selectMethod can no longer find the correct method. This first block below
puts the code in the context of a package:
fn <- "codefile.R"
writeLines(
c(
2006 May 22
2
confused by inheritance...
Hi r-devels,
I am stuck in some S4 inheritance problem:
setClass("A",representation(a="numeric"))
setClass("A1",representation(b="numeric"),contains="A")
setClass("A2",representation(c="numeric"),contains="A1")
if(!isGeneric("foo")){
setGeneric("foo", function(x,y,z, ...)
2008 May 10
2
Hashes as S4 Classes, or: How to separate environments
For learning purposes mainly I attempted to implement hashes/maps/dictionaries
(Python lingua) as S4 classes, see the coding below. I came across some rough S4
edges, but in the end it worked (for one dictionary).
When testing ones sees that the dictionaries D1 and D2 share their environments
D1 at hash and D2 at hash, though I thought a new and empty environment would be
generated each time
2020 Feb 19
2
Possible Regression in setClassUnion between 3.5.0 and 3.6.0
Thanks, I'll look into it.
On Tue, Feb 18, 2020 at 8:32 AM Ezra Tucker <ezztucker at gmail.com> wrote:
>
> Hi Robert,
>
> This looks like a bug to me (tested in R 3.6.2 on Windows), f(new("a"))
> should return "hi!". I'll add that this DOES work properly in 3.6.1
> which leads me to suspect this could be due to the subtle change in the
> way