Displaying 20 results from an estimated 2000 matches similar to: "S4 methods: unable to find an inherited method"
2007 Apr 02
0
Object problems with Generic and rematchDefinition
Hello all,
Let me try this again with some code.
I am trying to make a new object and it's not working. I get :
Error in rematchDefinition(definition, fdef, mnames, fnames, signature) :
methods can add arguments to the generic only if '...' is an
argument to the generic
as my error. I have included my code. It is from the xcms package.
Any help would be great even if
2007 Jan 19
3
if else statement
Hello,
I'm doing some scripting and I've noticed that R doesn't seem to
have an
if (cond){
do
}ifelse (cond) {
do
} else {
do
}
type block.
Is this correct or am I missing something.
THX
Paul
--
Research Technician
Mass Spectrometry
o The
/
o Scripps
\
o Research
/
o Institute
2007 Apr 15
1
unable to find inherited method for function "edges", for signature "ugsh", "missing"
I am new to using S4 methods and have run into this problem (on Windows XP using R 2.4.1): I am writing a package in which I use the graph package. I define my own classes of graphs as:
setOldClass("graphsh")
setOldClass("ugsh")
setIs("ugsh", "graphsh")
(I know that I "should have" used setClass instead - and I will eventually - but right now
2011 Jul 20
1
SSOAP & chemspider
Dear all,
I've been trying on and off for the past few months to get SSOAP to work with chemspider. First I tried the WSDL file:
cs<-processWSDL("http://www.chemspider.com/MassSpecAPI.asmx?WSDL")
Error in parse(text = paste(txt, collapse = "\n")) :
<text>:1:29: unexpected input
1: function(x, ..., obj = new( ?
^
In addition:
2008 Jan 07
4
side by side plots
Hello everyone,
I have an overlay plot it's nice but you can't see all the data. I would
like to know if there is a way to get a plot that gives a side by side
plot so that each plot would be next to each other. The two plots have
the same data are of different species. At the moment this is the code I'm
using:
exp<-cbind(abs(round(rnorm(10),2)*10), seq(100, 200, by=10))
2007 Jun 18
2
data type for block data?
Dear All,
I have a matrix with data that is not organised. I would like to go
through this and extract it. Each feature has 2 vectors which express
the data. I also have an index of the places where the data should be cut.
eg.
>class(cc)
"matrix"
>cc
[,1] [,2]
[1,] 1 26
[2,] 2 27
[3,] 3 28
[4,] 4 29
[5,] 5 30
[6,] 6 31
[7,] 7 32
2009 Jul 16
1
Handling masked methods
Hi,
Say I have two packages, test1 and test2, that both define the generic
method train (identical definition), and each has a specific train
method for a different S4 object (foo and bar, resp.)
I want to be able to call train(foo, x, y) and train(bar, x, y), which
doesn't work since test2 masks test1, as seen below.
The two solutions I can think of are to a) prefix train,
2007 Aug 10
1
reading xcms files
Hi,
I am using xcms library to read mass spectrum data. I generate objects from CDF files using the command line
> SME10 <- xcmsRaw("SME_10.CDF")
I have 50 CDF files with different name and I don't want to repeat the command for each one. Is there any option to read all the files and generate a corresponding object name?
In advance thank you
Roberto
[[alternative HTML
2013 May 08
1
Namespace/inheritance problem in S4 methods for a union class
Hi,
I started this post on bioc-devel but this seems to be more general:
https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html
See reproducible example from Martin below.
Thank you.
Renaud
---------- Forwarded message ----------
From: Martin Morgan <mtmorgan at fhcrc.org>
Date: 7 May 2013 19:55
Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem
in S4
2007 Aug 28
4
Nodes & edges with similarity matrix
Hello,
I apologise if someone has already answered this but I searched and
googled but didn't find anything.
I have a matrix which gives me the similarity of each item to each
other. I would like to turn this matrix into something like what they
have in the graph package with the nodes and edges.
http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find
a method to
2006 Nov 29
3
better define: matrix comparison and cbind issue
Hello,
Sorry to all for the lack of communication, and thanks to those with the
suggestions.
So I have two matrixes which are different sizes, same column number but
different row number.
What I would like to do is to compare A to B. In the 6 and 9th column there
are ref numbers (molecular masses to be exact). I would like to check A and
B by these columns. If I find that the number in A[9,x]
2011 Oct 10
1
pmml for random forest & rules
Hi,
I am having some trouble using R 2.13.1 for generating a pmml object
of of class "c('randomForest.formula', 'randomForest')"
I see that these methods are available:
> methods(pmml)
[1] pmml.coxph* pmml.hclust* pmml.itemsets* pmml.kmeans*
pmml.ksvm* pmml.lm* pmml.multinom* pmml.nnet*
pmml.rpart*
[10] pmml.rsf* pmml.rules* pmml.survreg*
2007 May 25
1
3D plots with data.frame
Dear all,
Thank you for any help. I have a data.frame and would like to plot
it in 3D. I have tried wireframe() and cloud(), I got
scatterplot3d(xs)
Error: could not find function "scatterplot3d"
> wireframe(xs)
Error in wireframe(xs) : no applicable method for "wireframe"
> persp(x=x, y=y, z=xs)
Error in persp.default(x = x, y = y, z = xs) :
(list)
2009 Dec 15
1
S4 dispatch and S3 "connection" objects
Hello,
I'm trying to get S4 dispatch on S3 "connection" objects.
So I do :
setOldClass( "connection" )
and then :
setGeneric( "bling", function(object) standardGeneric( "bling" ) )
setMethod( "bling", "connection", function(object) cat( "gotcha ",
as.integer(object), "\n" ) )
but I get :
f <- file(
2011 Feb 15
1
S4 problems
Hello everybody
[R-2.12.1]
I am having difficulty dealing with Oarray objects.
I have a generic function, call it foo(), and I wish
to define a method for Oarray objects.
I do not have or want a method for regular arrays [actually,
I want to coerce to an Oarray, and give a warning].
But setMethod() does not behave as desired, giving
an error message when I try to define a method for
Oarray
2009 Dec 03
1
S4 and head() problems
Hi
I am having difficulty defining an S4 method for head() and tail().
I can't quite provide minimal self-contained code
because the problem appears to require the whole corpus
of my package; and there also appears to be a difference
between sourcing the lines directly, and having them
installed in a package.
The lines in question (I think) are:
setClass("mdm",
2008 May 08
2
anova p value extraction
hello all,
Quick question, how do I get the p value out of the anova?
Thanks,
Paul
> pb<-aov(as.numeric(diff[5,16:33]) ~ grF)
> summary(pb)
Df Sum Sq Mean Sq F value Pr(>F)
grF 3 2.7860e+10 9.2867e+09 4.2236 0.02534 *
Residuals 14 3.0783e+10 2.1988e+09
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 '
2009 Aug 05
1
S4 method dispatch: coercion of arguments with setAs defined
Hi list,
I've got a class B that contains a slot obj of class A. I'd like to be
able to call all the methods of class A directly on objects of class B
as if I had called the method on slot obj. This without overloading all
methods of class A to work on class B.
I don't define B as an extension of A, because I want class B to also
work with objects of classes that inherit from
2012 Jun 14
1
readHTMLTable function - unable to find an inherited method ~ for signature "NULL"
Hi R experts,
I have been playing with library(XML) recently and found out that
readHTMLTable workls flawlessly for some website, but it does give me an
error like below
... Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "readHTMLTable", for
signature "NULL"
let's say..for example, this code works fine
a
2008 Mar 20
2
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
Hello Everyone,
I am writing programs in R from 7 months and I am able to solve most of the
errors/issues except for this current post.
My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains
the Microarray Expression Values collected from the Illumina Microarray
experiment. These collected intensity values need to be normalized(Rank
Invariant Normalization) by using the R