similar to: Disabling S4 primitive dispatch during method resolution affects namespace load actions

>>>>> Ivan Krylov via R-devel >>>>> on Fri, 27 Sep 2024 13:32:27 +0300 writes: > Hello, > This problem originally surfaced as an interaction between 'brms', > 'rstan' and 'Rcpp' [1]: a call to dimnames() from the 'brms' package on > an object of an S4 class owned by the 'rstan' package tried to

With the current version of the "raster" package (that I maintain), R CMD check on packages "soilDB" and "PopGenReport" have this NOTE: Package: soilDB Check: data for non-ASCII characters New result: NOTE Error in .requirePackage(package) : unable to find required package 'raster' Calls: <Anonymous> ... .findInheritedMethods ->

Hi all, in the help for RClassUtils I found the expression "privileged slots" in function "checkSlotAssignment" with the explanation: /privileged slots (those that can only be set by accesor functions defined along with the class itself)/ I thought all slots of a (not private) class can be a accessed by a user via the @ Operator. Is there a way to make a single slot of a

Hi again, Here is a very simplified version of a class hierarchy defined in the Biobase package (Bioconductor). I post here because this seems to be an S4 related problem: setClass("A", representation(name="character")) setMethod("initialize", "A", function(.Object) {.Object at name <- "I'm an A"; .Object})

Hi, I got the following error. Sorry but this time I couldn't reproduce it with a simple chunk of code: .TM.repl.i.2col(): drop 'matrix' case ... Error in .nextMethod(x = x, i = i, j = j) : 'i' has no integer column number should never happen; please report In addition: Warning messages: 1: Ambiguous method selection for "%*%", target

There are too many arguments in the signature of the my_inla generic. The signature defaults to every argument in the formals, which are probably already over-specified. Typically, one defines a generic with the formals (x, ...), or perhaps in this case (x, model, ...), but more on that below Unrelated to this issue, the my_inla generic is defined incorrectly. It should call

Hello everybody R version 2.4.0 alpha (2006-09-15 r39323), MacOSX 10.4.7 Next S4 problem. I have "brob" objects that are large real numbers, and now I want "glub" numbers that are to be a pair of glubs that represent complex numbers. I want to define binary operator "+" so that if either the left or right argument are glubs, it uses .ArithGlub. If either

I am extending a DBI connection by setClass("TSPostgreSQLConnection", contains=c("PostgreSQLConnection","TSdbOptions")) but the first time I use this I am getting a warning when it tries to coerce the TSPostgreSQLConnection to a PostgreSQLConnection. After the first use the warning stops, but the first warning is causing me problems when I do automatic checks

Dear all, I'm trying to create a virtual S4 class with some subclasses. I noticed that adding slots to this class increases the memory use and slows the functions down. Note that I'm adding very small slots (integer or character both of length 1). I've made a reproducible example at https://github.com/ThierryO/testvirtualclass. The R CMD check --as-cran fails on the tests. Some of

Dear all, I did some more work in this. - put all the metadata in a dedicated subclass (see metadataclass branch in github repository). This doesn't solve the problem. - test the code under R 3.1.2. This gives the same problem. So this is NOT a bug introduced by R 3.2.0 :-) - Profiling the code. Below the summary (code is on GitHub). It seems like most of the time is spent by paste(). Note

I have a little problem about method dispatch and "unnessary" copying. Basically what I would like to do is: `[.myclass` <- function(x, i,j, extraopt=TRUE/FALSE, drop=TRUE) { ...do stuff depending on extraopt... value <- Nextmethod("[", x, i,j, drop=TRUE) ... do more stuff depending on extraopt... } I have two general problems: (1) NextMethod() really

These lines of code setClass("A", representation(x="numeric")) setMethod(initialize, "A", function(.Object, ...) stop("oops")) setClass("B", representation("A")) result in > setClass("B", representation("A")) Error in initialize(value, ...) : oops in R version 2.9.0 alpha (2009-03-28 r48239) R version 2.10.0

Hi, I recently ran into this problem. I couldn't find any mention of it in the setClass documentation. setClass("Foo", representation(file = "character")) setMethod("initialize", "Foo", function(.Object, file) { print(file) }) setClass("Bar", contains = "Foo") And the error: Error in print(file) : argument "file" is

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*

Hello Folks, When I run the document below through sweave, rgui.exe/rsession.exe leaves a file handle open to the sweave-001.pdf graphic (as verified by process explorer). Pdflatex.exe then crashes (with a Permission Denied error) because the graphic file is locked. This only seems to happen when there is an error in the sweave document. When there are no errors, no file handles are left open.

Dear friends - I'm having troubles with nlme fitting a simplified model as shown below eliciting the error Error in chol.default((value + t(value))/2) : ? the leading minor of order 1 is not positive definite - I have seen the threads on this error but it didn't help me solve the problem. The model runs well in brms and identifies the used parameters even with fixed effects for TRT?

I should add one more item that may be related here -- calling 'methods:::.requirePackage' returns a different result based on whether the package namespace is already loaded or not. If the package namespace is not loaded, the package is loaded and attached, and the package environment is returned: > methods:::.requirePackage("digest") Loading required package:

(Just returning from the "wilds" of Canada, so not able to comment on the specifics, but ...) There is a basic point about generic functions that may be related to the "private" class question and my earlier remarks that Martin alluded to. R (and S4 before it) allows packages to define methods for a generic function in another package. Say, for plot() in graphics. The

>>>>> Kevin Ushey <kevinushey at gmail.com> >>>>> on Fri, 29 Jul 2016 11:46:19 -0700 writes: > I should add one more item that may be related here -- > calling 'methods:::.requirePackage' returns a different > result based on whether the package namespace is already > loaded or not. > If the package namespace is

Dear Colleagues: In an attempt to have things like # See page \pageref{this} inside comments in R code chunks I have modified Sweave.sty as below. I have followed fancyvrb's manual with regard to the use of the commandchars argument. But when compiling with LaTeX (using attached test file) I get a LaTeX error (/usr/share/texmf-texlive/tex/latex/ae/t1aett.fd) ! Missing \endcsname