Displaying 20 results from an estimated 3000 matches similar to: "inspect s4 methods"
2007 May 27
2
[Bioc-devel] promptClass
promptClass fails to identify methods associated with the class. Here
is a fix:
Index: promptClass.R
===================================================================
--- promptClass.R (revision 41719)
+++ promptClass.R (working copy)
@@ -165,7 +165,7 @@
if (nmeths > 0) {
.meths.body <- " \\describe{"
for (i in 1:nmeths) {
- .sigmat
2009 Jul 29
1
RFC: methods() and showMethods() {was "debug"}
(a new thread, on purpose)
>>>>> "RobG" == Robert Gentleman <rgentlem at fhcrc.org>
>>>>> on Mon, 27 Jul 2009 16:55:50 -0700 writes:
RobG> Hi, I just committed a change to R-devel so that if
RobG> debug is called on an S3 generic function, all methods
RobG> will also automatically have debug turned on for them
RobG>
2005 Jun 02
1
showMethods doubt
Hi,
I'm developing in S4 and I wanted to see the methods for a specific
class using showMethods but I didn't succed. Can someone help ? See the
example below.
setClass("myclass",
representation(
name ="character"
)
)
setGeneric("mymeth", function(obj, ...){
standardGeneric("mymeth")
}
)
setMethod("mymeth",
2006 Oct 17
1
Caching bug with showMethods?
showMethods isn't reporting inherited methods when it is first
called. The methods are there and after calling them, showMethods
gives the right output.
Here is an example (using R-devel r39647):
setClass("A", representation(x="numeric"),
prototype=list(x=1))
setClass("B", contains="A",
prototype=list(x=2))
2009 Feb 25
1
Unexpected side effect of the ":::" operator on the value of isGeneric
Hi,
when running the following on a fresh R,
library("IRanges")
annotation
showMethods("annotation")
Biobase:::annotation
showMethods("annotation")
I get (see the "^^^^^" marked output at the bottom):
> library("IRanges")
Carico il pacchetto richiesto: 'IRanges'
The following object(s) are masked from package:base :
2010 Jan 25
1
reshape package cast() function
Hi all,
I think I'm cracking up. Please help me understand why I'm getting
different results with m.test and m.test2 in the example below.
> library(reshape)
Loading required package: plyr
>
> m.test <- data.frame(id = factor(rep(1:10, 2)), variable=rep(c("var1","var2"),10), value=rnorm(20))
> cast(m.test, ...~variable, value="value") ## cast
2016 Apr 20
0
Matrix: How create a _row-oriented_ sparse Matrix (=dgRMatrix)?
>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>
>>>>> on Tue, 19 Apr 2016 14:04:11 -0700 writes:
> Using the Matrix package, how can I create a row-oriented sparse
> Matrix from scratch populated with some data? By default a
> column-oriented one is created and I'm aware of the note that the
> package is optimized for
2009 Aug 25
2
how to pass user input to a function?
Hi everyone,
I'm building a website (http://yourpsyche.org) using Jeffrey Horner's
awesome Rapache module. I want to take user input, and pass it to an R
script. At first I was simply using if else statements, but after a
while I had so many nested if else's in my code that my head was
spinning. So then I started using cat() and source() to write
temporary files and read them back in
2009 Oct 25
1
A naive question about permutation tests in the coin package
Dear R helpers,
I am trying to understand how to use the independence_test function in
the coin package. I think I suffer from a misunderstanding about what
the package does. Either that or I do not understand how to use it
properly. Specifically, I cannot understand if I can test independence
of arbitrary statistics.
Take the following example:
set.seed(10)
d <- data.frame(y = c(rnorm(10,
2012 Apr 24
2
How do i read the source code of "biplot"?
> biplot
standardGeneric for "biplot" defined from package "stats"
function (x, ...)
standardGeneric("biplot")
<environment: 0x0d4444d8>
Methods may be defined for arguments: x
Use showMethods("biplot") for currently available ones.
>
>
> showMethods("biplot")
Function: biplot (package stats)
x="ANY"
2003 Sep 05
2
S4 Method Collisions with "[" (PR#4075)
Full_Name: Colin A. Smith
Version: 1.8.0
OS: Mac OS X 10.2.6
Submission from: (NULL) (216.102.90.18)
Both Biobase and my package annaffy use S4 classes to define methods for "[".
Both packages use the save image method of installation. (See annaffy 1.0.3 in
BioC CVS.)
Depending on how both packages are loaded, the Biobase definitions seem to be
getting masked out:
>
2012 Mar 24
2
RC / methods package
(I think this is being caused by the new methods package in RC.)
In the RC (March 24) some of my packages are generating a Note
Note: Method with signature "MySQLConnection#integer" chosen for
function "coerce",
target signature "TSMySQLConnection#integer".
"dbObjectId#integer" would also be valid
This is coming from a call to dbGetQuery() in package
2014 Jul 11
1
Namespaces and S4 Generics
I've installed R-devel
R Under development (unstable) (2014-07-09 r66111)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
and am trying to resolve some problems that I am seeing with my
SparseM package. In prior versions I explicitly had:
setGeneric("image", function(x, ...) standardGeneric("image"))
and then used setMethod to define a method for the class matrix.csr
but
2012 Aug 22
1
loading both RPostgreSQL and RSQLite leads to problems
hello,
if i load the RSQLite package in addition to the RPostgreSQL package,
i get various errors when trying to use RPostgreSQL functions. here is
an example transcript showing one such error:
==========================================================
R version 2.15.0 (2012-03-30)
[...]
> packageVersion('RPostgreSQL')
[1] 0.3.2
> packageVersion('RSQLite')
[1] 0.11.1
2010 May 21
1
S4 method defined but not used
Dear R developers,
I am having a slightly weird issue with a S4 method defined in my package adegenet 1.2-4, with R 2.11.0. As far as I know, the problem is new, and the code implementing the method has not changed for more than a year and worked well so far.
The problem is the following. I define, in the package, a method "[" for the S4 class 'genind'. The method's
2009 Aug 26
1
Problem with standard generic methods in Matrix package
I have posted this message on r-lang, but it is perhaps more appropriate
on r-devel:
---
Hello,
I'm puzzled by a problem with call to diag(), rowSums(), rownames() on
objects of class "dgtMatrix", created by sparseMatrix() or spMatrix().
I use Matrix 0.999375-30.
The weird thing is that I don't encounter any problem when I use this
functions on the R prompt, or
2011 Aug 23
0
Matrix:::qr.qy and signature(qr = "sparseQR", y = "dgCMatrix")
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_0.999375-50 lattice_0.19-30
loaded via a namespace (and not attached):
[1] grid_2.13.1
2002 Nov 05
1
function showMethods and inheritance
Hi,
The following question might come from my (deep) misunderstanding
of the concepts in the package 'methods'.
I have a class 'A', and a class 'B' inheriting 'A' (so defined
with 'setClass' and the parameter 'contains="A"'. The class
A has a method 'mymethod'. A call to 'showMethods("mymethod")'
return the
2011 Mar 04
3
Generic mixup?
Hello list.
This is from an R session (admittedly, I''m still using R 2.11.1):
> print
function (x, ...)
UseMethod("print")
<environment: namespace:base>
> showMethods("print")
Function "print":
<not a generic function>
Don''t the two results contradict each other? Or do I have a terrible
misunderstanding of what
2006 Apr 09
2
type converters not being saved to workspace
Any one can explain why this happens or any work arounds?
> setClass('foo')
[1] "foo"
> setAs('foo', 'character', function(from) from)
> showMethods('coerce')
Function "coerce":
from = "ANY", to = "array"
from = "ANY", to = "call"
from = "ANY", to = "character"
from =