similar to: Overloading S4 methods

Hi, Strange things happen. Here is a simple example: > setClass("A", contains="integer") > setMethod("as.matrix", "A", function(x, ...) t(callNextMethod())) Creating a generic function for ?as.matrix? from package ?base? in the global environment [1] "as.matrix" > a <- new("A", 1:3) > as.matrix(a)

Dear all, After installing R 2.4.0, a definition of "[" for an S4 class has stopped working as the default for drop in the generic, TRUE, appears to override the default in the method The method is defined for demonstration purposes as setMethod("[", signature(x="FLQuant"), function(x, i="missing", j="missing", k="missing",

Hi, A lowess method is defined in our package for one of our S4 classes. To explicitely define the generic this is being used if (!isGeneric("lowess")) setGeneric("lowess", useAsDefault = lowess) This works fine for many other methods inherited from various R packages. In this case a warning is issued in R CMD check: * checking R code for possible problems ... NOTE

Hi, I have a S3 package with namespace called "myS3Pkg". Inside my package I would like to create a S4 class which extends (adds 2 slots) another S4 class from some other package. The class should be created in "myPkg" environment (and not global environment). Using: setClass("myS4class", representation("otherS4class", mydata = "numeric"),

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

please see the code below. foo2 fails to dispatch correctly, but foo does fine. i have tried 'cacheMetaData(1)' and a number of different variants of 'cacheGenericsMetaData', on the possibility there is a caching issue. but i still can't sort it out. also one general question: does it really matter what's in the body of the function definition in a

Here is an example: setGeneric("foo", function(x, y) standardGeneric("foo")) setMethod("foo", c("numeric", "ANY"), function(x, y) cat("I'm the foo#numeric#ANY method\n") ) Dispatch works as expected but selectMethod() fails to find the method: > foo(1, TRUE) I'm the foo#numeric#ANY method >

Generally you'd use file() to open the file, then use readLines(), say inside a while() loop to read one `chunk' at a time. However, your example looks a bit strange. The possibility of empty line makes it a bit more complicated, by that last couple of lines seems to suggest that you could have a line of data follow by another line of data without variable label. If that's true, I

Hi Michael, Thanks for looking into this. I suspect that truncation of ANY suffixes from method signatures is also the culprit behind the sudden breakage of aliases of the form \alias{foo,numeric-method} when a method without the ANY suffix in its signature gets added to the ecosystem. See my post about this to the Bioc-devel mailing list a couple of months ago:

Dear all, I need to re-define some mathematical operators (+, *, /, etc) for an S4 class based on array. All references I have found (S Programming, Green Book) show how to define S3 methods for this (like in page 89 of S Programming for "-.polynomial"). What is the preferred S4 way for doing this? I hope I haven't missed some obvious piece of documentation. Many thanks, Iago

Fine with me as long as eliminating the inconveniences associated with it can be put on the roadmap. The alias instability and the fact that the user has no way to know if s/he should do ?`foo,numeric-method` or ?`foo,numeric,ANY-method` to find the method has been a long-standing problem. H. On 3/21/19 21:29, Michael Lawrence wrote: If we started over, I'd try to avoid this sort of

Hi, First a bit of disclaimer... I haven't isolated this problem into an easy to reproduce case, and I won't be surprised if the root cause is a fault in my code's use of name spaces or some such. The error I'm seeing is one in which the desired method is not found. What worries me in terms of my expectations of how to debug the problem is that showMethods and selectMethod both

Hello, I am about to move all of my modelling work into R, and I have been investigating the present state of MCMC and Bayesian methods in R. Following a thread on the mailing list in 2000, I have looked at mcmcpack and Hydra. Three years down the line, is there anything new in this area? I have used both MCSim and WinBUGS in the past. The first one seems promising, but is too focused towards

Hello, I am trying to use Yan and Rossini's Makefile for cross building Windows versions of R packages in Linux with R 1.9.0. When compiling R with the mingw tools I get an error about expm1 being undeclared when first found at src/main/arithmetic.c:1019 If I fiddle a bit with it later on I also get errors about log1p bein undeclared. Any idea what should I look for? I am using R 1.9.0 in

Hello, I am trying to use Yan and Rossini's Makefile for cross building Windows versions of R packages in Linux with R 1.9.0. When compiling R with the mingw tools I get an error about expm1 being undeclared when first found at src/main/arithmetic.c:1019 If I fiddle a bit with it later on I also get errors about log1p bein undeclared. Any idea what should I look for? I am using R 1.9.0 in

Hello, Am I right in thinking the cross-compilations tools, kindly maintained by Prof Ripley, are still waiting to be updated for 2.7.0? Thanks, Iago -- Iago Mosqueira Cefas Systems Modelling Pakefield Rd. Lowestoft NR33 0HT U.K. +44 (0)1502 558003

Dear all, When creating a bundle with some internal dependencies (package B in bundle depends on package A), would having the same version installed suffice? Can I ignore the dependencie in package B's description? The test of package B fails when calling data() for an object in pacakge A, so I am not sure right now whether the whole dependencie is not being met or simple relates to data().

Hello, I am trying to draw a key inside a single panel in a lattice xyplot. The panel function uses panel.number() to use a slightly different style for one of the panels. Once inside than panel I am using draw.key(list(text=list(lab='catch'), lines=list(lwd=c(2)), text=list(lab='landings'), rectangles=list(col=rgb(0.1, 0.1, 0, 0.1)), x=0,

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

Hi, In the situation below the note issued by the dispatch algo doesn't seem right: setClass("A", representation(stuff="complex")) setAs("ANY", "A", function(from) new("A", stuff=as.complex(from))) > as(6, "A") An object of class "A" Slot "stuff": [1] 6+0i > as(6L, "A")