similar to: inspect s4 methods

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

(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>

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

>>>>> 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

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

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,

Hello. I am trying to optimize a set of parameters using /optim/ in which the actual function to be minimized contains matrix multiplication and is of the form: SUM ((A%*%X - B)^2) where A is a matrix and X and B are vectors, with X as parameter vector. This has worked well so far. Recently, I was given a data set A of size 360440 x 1173, which could not be handled as a normal matrix. I

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: >

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

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

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

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",

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))

Dear all, I'm getting more and more frustrated with the whole S4 thing and I'm looking for a more advanced summary on how to deal with them. Often I get error messages that don't make sense at all, or the code is not doing what I think it would do. Far too often inspecting the code requires me to go to the source, which doesn't really help in easily finding the bit of code

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 :

>>>>> C W <tmrsg11 at gmail.com> >>>>> on Fri, 20 Oct 2017 15:51:16 -0400 writes: > Thank you for your responses. I guess I don't feel > alone. I don't find the documentation go into any detail. > I also find it surprising that, >> object.size(train$data) > 1730904 bytes >>

Hi all. I am currently attempting to build a list of sparse matrixes. That I have already achieved, by > vmat <- list() > for (i in 1:n) { > vmat <- c(vmat, sparseMatrix(i,j,x=data) > } How I am trying to select those elements from the list where the column e.g. 999 is not null. I can do this for one of the sparse matrices with > which(vmat[[1]][,999] != 0) which

Hello, If I want to see how, say, apply function is written, how would I be able to do that? Just typing "apply" at the prompt does not work. Thank you for help! Sergey

Dear All, in some functions of my package, I use the Matrix S4 class, as defined in the Matrix package. I don't want to depend on Matrix, however, because my package is perfectly fine without Matrix, most of the functionality does not need Matrix. Matrix is so included in the 'Suggests' line. I load Matrix via require(), from the functions that really need it. This mostly works

> On Oct 21, 2017, at 7:50 AM, Martin Maechler <maechler at stat.math.ethz.ch> wrote: > >>>>>> C W <tmrsg11 at gmail.com> >>>>>> on Fri, 20 Oct 2017 15:51:16 -0400 writes: > >> Thank you for your responses. I guess I don't feel >> alone. I don't find the documentation go into any detail. > >> I also find