similar to: Problem with S3 method dispatch and NAMESPACE

I am cleaning up the rms package to not export functions not to be called directly by users. rms uses generic functions defined in other packages. For example there is a latex method in the Hmisc package, and rms has a latex method for objects of class "anova.rms" so there are anova.rms and latex.anova.rms functions in rms. I use:

Hi, from the man page ?methods, I expected to be able to build pairs (class,package) for a given S3 method, e.g., print, using attr(methods(print), 'info'). However all the methods, except the ones defined in base or S4 methods, get the 'from' value "registered S3method for print", instead of the actual package name (see below for the first rows). Is this normal

PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods indicates that one should setGeneric("unique") setClass("A") unique.A <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "A", unique.A) Both S3 and S4 methods need to be exported in the NAMESPACE import(methods) S3method(unique, A)

I am writing my first R package, and I have been getting the following series of errors when I run R CMD check: * checking S3 generic/method consistency ... WARNING Error: package/namespace load failed for 'REEMtree' Call sequence: 2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)), call. = FALSE, domain = NA) 1: library(package,

1. A Surv object is a matrix with some extra attributes. The as.matrix.Surv function removes the extras but otherwise leaves it as is. 2. The last several versions of the survival library were accidentally missing the S3method('as.matrix', 'Surv') line from their NAMESPACE file. (Instead it's position is held by a duplicate of the line just above it in the NAMESPACE file,

Dear List, In one of my packages I have an S3 method for the plot3d generic function from package rgl. I am trying to streamline my Depends entries but don't know how to have plot3d(foo) in the examples section for the plot3d method in my package, without rgl being in Depends. Note that I importFrom(rgl, plotd3d) and register my S3 method via S3Method() in the NAMESPACE. If rgl is not in

Hello, I try to set up namespaces for packages. It is fine for several of them, except one whose compilation fails (under Windows XP & R 2.0.0): ---------- Making package svViews ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata Error in parse(file, n, text, prompt) : syntax error on line 21 Execution halted make[2]: *** [nmspace] Error 1 make[1]: ***

Dear All, In R 3.6.3 (and earlier), method dispatch used to work for methods stored in local environments that are attached to the search path. For example: myfun <- function(y) { out <- list(y=y) class(out) <- "myclass" return(out) } print.myclass <- function(x, ...) print(formatC(x$y, format="f", digits=5)) myfun(1:4) # prints: [1]

Dear all, I have defined a generic as.ff(x, ...) and a method as.ff.function(x, ...) which converts a standard R function x into a chunked version operating on large ff objects. Everything works fine, but when registering S3method("as.ff",function) in NAMESPACE, the installation fails with some kind of parsing error: adding build stamp to DESCRIPTION installing NAMESPACE file

Hi all, The profr package provides a method for displaying its output with ggplot: ggplot.print. You don't need this ggplot2 to use profr, so ggplot2 is listed under enhances in the DESCRIPTION file. If I have just S3method(ggplot, profr) in my NAMESPACE, then I get: ** testing if installed package can be loaded Error : object 'ggplot' not found whilst loading namespace

Dear all, I am developing a package, which bundles my most frequently used functions. One of those is a modified version of droplevels from the base package (basically, it preserves any contrast function which was used to create the factor, contrast matrices are not kept, for they could be wrong if a level is dropped). In my NAMESPACE file I've the following directives, which should export

Dear Wolfgang, I think this new behaviour is related to the following R 4.0.0 NEWS item: > S3 method lookup now by default skips the elements of the search path between the global and base environments. Your environment "myenv" is attached at position 2 of the search() path and thus now skipped in S3 method lookup. I have just noticed that

CCing r-devel. On Tue, 14 May 2019 at 02:11, Pavel Krivitsky <pavel at uow.edu.au> wrote: > > Dear All, > > I've run into this while updating a package with unfortunately named > legacy functions. It seems like something that might be worth changing > in R, and I want to get a sense of whether this is a problem before > submitting a report to the Bugzilla. > >

Hello, I have a general question about combining imputations as well as a question specific to the rms and Hmisc packages. The situation is multiple regression on a data set where multiple imputation has been used to give M imputed data sets. I know how to get the combined estimate of the covariance matrix of the estimated coefficients (average the M covariance matrices from the individual

Dear all, I would like to know whether any specification test for linear against nonlinear model hypothesis has been implemented in R using the quantreg package. I could read papers concerning this issue, but they haven't been implemented at R. As far as I know, we only have two specification tests in this line: anova.rq and Khmaladze.test. The first one test equality and significance of

In this post https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html a package author reports that S4 dispatch fails. I can reproduce this with a PkgA (attached; 'intervals' is a relatively light-weight CRAN package) that has DESCRIPTION with Depends: intervals Imports: graphics NAMESPACE: importFrom(graphics, "plot") export("plot")

R-exts.pdf discribes S3method a little bit. But I want to understand more on how it is called, implemented and when to use it. I don't find it in an R session. But I see S3method() in some NAMESPACE files. > S3method Error: object 'S3method' not found > ?S3method No documentation for 'S3method' in specified packages and libraries: you could try '??S3method' I

On Tue, 14 May 2019 at 12:31, Pavel Krivitsky <pavel at uow.edu.au> wrote: > > > Note that disabling name-based dispatch implies two things: 1) the > > inability to override your method by defining gen.formula in the > > global environment, and 2) another package can break yours (i.e., > > internal calls to gen()) by registering an S3 method for gen() after >

I agree, this is a good idea and would be very helpful in interactive contexts. I have a draft patch implementing this feature here: https://github.com/r-devel/r-svn/pull/122 (Append ?.patch? to the URL to get a raw patch.) Regards, Tomasz > On Mar 31, 2023, at 2:11 PM, Karolis K <karolis.koncevicius at gmail.com> wrote: > > Hello, > > In the current R-devel @ is S3

[Env: R 2.11.1, Win Xp, using Eclipse/StatET] In a package I'm working on, I want to create as.matrix() and as.array() methods for a particular kind of object (log odds ratios). These are returned in a loddsratio object as the $coefficients component, a vector, but really reflect an underlying (R-1)x(C-1)xstrata array, whose attributes are contained in other components. I define coef,