[R-pkg-devel] Unneeded S3 method registration

Dear R package developers My emmeans package failed preliminary checks when I submitted an update today, apparently due to a recent change in requirements on method registration. The message I got was: * checking S3 generic/method consistency ... NOTE Apparent methods for exported generics not

[R-pkg-devel] Examples with conditional blocks

Dear package developers, What is the best way to provide examples in help pages that should only be run under certain conditions -- e.g., whether another package is installed? The code that is run conditionally is then an expression, so only the results of the last statement are displayed; and

Re: [Rd] [External] Re: svd() results should have a class

the returned object be of class c("svd", "list"). Best, Russ -Original Message- From: Duncan Murdoch Sent: Thursday, June 23, 2022 7:23 PM To: Lenth, Russell V ; Robert Harlow Cc: r-devel@r-project.org Subject: Re: [Rd] [External] Re: svd() results should have a class On

Re: [R-pkg-devel] [External] Re: What is a "retired"package?

dependable. But one difference in retirement is that I now care less about public embarrassment, such as not knowing that all along, I could have used base::apply instead of plyr::aaply. -Original Message- From: Hadley Wickham Sent: Tuesday, September 21, 2021 11:48 AM To: Lenth, Russell V

Re: [R-pkg-devel] [External] Re: What is a "retired"package?

OK. Well, as Noah has pointed out, I can just use apply to do what I need, and get plyr out of the picture. But for the broader question, Jeff is saying that there really are 700 packages that are in potential trouble! __

Re: [R-pkg-devel] [External] Re: What is a "retired"package?

... "I am not fixing this hot mess"??? To the contrary, the README contains a clearly expressed intention to maintain plyr to keep in on CRAN. RL -Original Message- From: Jeff Newmiller Sent: Tuesday, September 21, 2021 10:36 AM To: r-package-devel@r-project.org; Lenth, Russ

Re: [R-pkg-devel] [External] Re: What is a "retired"package?

From: Andrew Simmons akwsi...@gmail.com > Doesn't apply already work on any dimensional arrays using argument MARGIN? Egads, yes it does! I can't explain why I didn't know that... Russ [[alternative HTML version deleted]]

[R-pkg-devel] What is a "retired"package?

I received a request that I remove the 'plyr' package from the Imports for my package, because plyr is retired. Indeed, the README file for plyr states: > plyr is retired: this means only changes necessary to keep it on CRAN will be made. > We recommend using dplyr (for data frames) or

[R-pkg-devel] Redirect error in .Rd file

Hello package developers, I just upgraded to R version 4.1.0, and now get a new error when I re-build my package. Among the messages about converting help files, I now get: ... update.emmGrid html REDIRECT:topic levels<-.emmGrid ->

Re: [R-pkg-devel] Documenting courtesy S3 methods

PM To: Lenth, Russell V Subject: Re: [R-pkg-devel] Documenting courtesy S3 methods Probably unnecessary to say, but if/when you determine whether the package must be installed, let us all know. Bert __ R-package-devel@r-project.org mailing list https

Re: [R-pkg-devel] Documenting courtesy S3 methods

seems that actually showing that in the Usage section is by far the clearest way to communicate that requirement. Russ From: Bert Gunter Sent: Wednesday, August 5, 2020 9:31 PM To: Lenth, Russell V Cc: r-package-devel@r-project.org Subject: [External] Re: [R-pkg-devel] Documenting courtesy S3

[R-pkg-devel] Documenting courtesy S3 methods

Dear package developers, My package offers a few methods whose generics are in other packages; for example, 'cld', for which the generic is in the 'multcomp' package. Unless the user wants to use cld() (which I don't even encourage), they do not need the multcomp package to use other features

Re: [R-pkg-devel] [External] Re: Farming out methods to other packages

, August 10, 2019 3:15 PM To: Lenth, Russell V Cc: Duncan Murdoch ; Iñaki Ucar ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] [External] Re: Farming out methods to other packages You could have your default method handle the cases you can handle; if you want that to dispatch you can

Re: [R-pkg-devel] [External] Re: Farming out methods to other packages

Thanks, Duncan. That's helpful. In addition, I confess I had a closing parenthesis in the wrong place. Should be:. . . .GlobalEnv), silent = TRUE) Cheers, Russ -Original Message- From: Duncan Murdoch Sent: Saturday, August 10, 2019 2:43 PM To: Lenth, Russell V ; Iñaki Ucar

Re: [R-pkg-devel] [External] Re: Farming out methods to other packages

Thanks, Neonira. Always something new to learn! Russ From: neonira Arinoem Sent: Saturday, August 10, 2019 2:22 PM To: Lenth, Russell V Cc: Iñaki Ucar ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] [External] Re: Farming out methods to other packages What about turning your S3

Re: [R-pkg-devel] [External] Re: Farming out methods to other packages

H, I thought of an approach -- a kind of manual dispatch technique. My generic is recover_data <- function(object, ...) { rd <- try(getS3method("recover_data", class(object)[1], envir = .GlobalEnv, silent = TRUE)) if (!inherits(rd, "try-error")) rd(object, ...) else

Re: [R-pkg-devel] [External] Re: Farming out methods to other packages

function that makes it really easy for other package developers to register their methods. It's based on similar code to what you point to.) Russ -Original Message- From: Iñaki Ucar Sent: Saturday, August 10, 2019 1:09 PM To: Lenth, Russell V Cc: r-package-devel@r-project.or

[R-pkg-devel] Farming out methods to other packages

Dear developers, I maintain a package, emmeans, that provides post-hoc analyses for a variety of models. These models are supported by writing S3 methods for recover_data and emm_grid. Quite a few models are supported internally in emmeans, but it would really be better if the packages that

Re: [Rd] [External] Re: quiet namespace load is noisy

ject.org/web/packages/afex/vignettes/afex_plot_introduction.html Best, Henrik Am Di., 23. Juli 2019 um 14:52 Uhr schrieb Ben Bolker mailto:bbol...@gmail.com>>: Does setting message=FALSE in the chunk options of the vignette help? Or less preferably, using supressMessages() ? On 2019-07-23 9

Re: [Rd] [External] Re: quiet namespace load is noisy

ormal behaviour, for which > it makes sense to suppress the message. This does not imply the > S3 overriding message should be suppressed as well. > > Best, > Lionel > > >> On 23 Jul 2019, at 06:29, Lenth, Russell V wrote: >> >> Dear R-devel,

[Rd] quiet namespace load is noisy

Dear R-devel, Consider the following clip (in R version 3.6.0, Windows): > requireNamespace("ggplot2", quietly = TRUE) Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang It seems to

[R-pkg-devel] pandoc version used in winbuilder

All, How does one tell what version of pandoc is being used by winbuilder (and probably other related CRAN-submission processes)? I have a package with several HTML vignettes, for which I use a custom style. I had decided to add the pandoc option '-strip-comments' to my script (my vignettes

Re: [Rd] [External] re: default for 'signif.stars'

rom: Abs Spurdle Sent: Thursday, March 28, 2019 12:19 AM To: Lenth, Russell V ; r-devel Subject: [External] re: [Rd] default for 'signif.stars' I read through the editorial. This is the one of the most mega-ultra-super-biased articles I've ever read. e.g. The authors encourage Baysian methods, and

[Rd] default for 'signif.stars'

Dear R-Devel, As I am sure many of you know, a special issue of The American Statistician just came out, and its theme is the [mis]use of P values and the many common ways in which they are abused. The lead editorial in that issue mentions the 2014 ASA guidelines on P values, and goes one step

Re: [Rd] Model formulas with explicit references

2)) Error in factor(cyl) : object 'cyl' not found I still suggest that predict(..., newdata = ...) should *always* return an error when newdata does not provide new values of the model data. Russ -Original Message- From: Berry, Charles Sent: Saturday, July 21, 2018 12:02 PM To: Lenth, Russ

[Rd] Model formulas with explicit references

Dear R-Devel, I seem to no longer be able to access the bug-reporting system, so am doing this by e-mail. My report concerns models where variables are explicitly referenced (or is it "dereferenced"?), such as: cars.lm <- lm(mtcars[[1]] ~ factor(mtcars$cyl) + mtcars[["disp"]]) I have

Re: [R-pkg-devel] More on explosive dependencies

to try it myself. Can I just ask what goes in your namespace file (and what roxygen tags you use) for the relevant methods? David On Tue, 17 Jul 2018 at 02:29, Lenth, Russell V mailto:russell-le...@uiowa.edu>> wrote: Thanks to all who responded. I am pleased to say that with your help, I h

Re: [R-pkg-devel] More on explosive dependencies

to be registered. Russ Russell V. Lenth  -  Professor Emeritus Department of Statistics and Actuarial Science The University of Iowa  -  Iowa City, IA 52242  USA   Voice (319)335-0712 (Dept. office)  -  FAX (319)335-3017 -Original Message- From: Lenth, Russell V Sent: Sunday,

[R-pkg-devel] More on explosive dependencies

Package developers, I posted a question a couple of months ago dealing with how to reduce the number of dependencies in a package. Part of the specific issue I face is that I have a `cld` S3 method for which the generic is in the multcomp package, but I don't want to import multcomp because it

Re: [R-pkg-devel] Courtesy methods and explosive dependencies

> There can't really be an "ImportGenerics", because S3 is so informal. A > generic function is a function that calls UseMethod, but it can do anything > else as well. So R would need some fancy code analysis to know whether it > was safe to import the generic but not all the dependencies of

Re: [R-pkg-devel] Courtesy methods and explosive dependencies

, but that aren't actually used by the method. I certainly wasn't trying to diss multcomp; that was just a concrete illustration. Russ -Original Message- From: Martin Maechler [mailto:maech...@stat.math.ethz.ch] Sent: Friday, May 25, 2018 2:13 AM To: Lenth, Russell V <russell

[R-pkg-devel] Courtesy methods and explosive dependencies

Package developers, I am trying to severely cut down on the number of dependencies of my package emmeans. It is now 48, which is quite a few (but that is down from over 100 in the preceding version, where I made the unwise choice of including a particularly greedy package in Imports). I hate

[R-pkg-devel] Indexing HTML vignette topics

Developers, I have a package that has a number of vignettes with examples and such; so I see an increasing need to provide easier ways to navigate among them and to find a particular topic. All the vignettes are written using R Markdown, subsequently converted to HTML. I did some searching

[R-pkg-devel] Annoying "missing file link" messages when rebuilding

Developers: Lately (the past month or so), I have been getting a ton of messages like the following whenever I rebuild my package: Rd warning: H:/progs/R/devel/EMMEANS/emmeans/man/xtable.emmGrid.Rd:57: missing file link 'print.xtableList' The flagged line 57 in xtable.emmGrid.Rd looks

[R-pkg-devel] Migrating a package name

Hello, I have a package 'lsmeans' (for "least-squares means") for follow-up analyses of models; and it has become increasingly clear to me that its name is archaic and misleading. It works for GLMs, ordinal and count regression, Bayesian models fitted using MCMC, and all sorts of other models

[R-pkg-devel] Re-exporting S3 generics

Dear package developers: My 'lsmeans' package provides, among other things, 'as.mcmc' and 'as.mcmc.list' methods for its 'ref.grid' objects. Those methods allow obtaining posterior predictions, or averages thereof, from certain models fitted using MCMC methods. My question concerns this: the

Re: [R-pkg-devel] Any new developments on "apparent S3 method" issue?

n may not be very straightforward to implement. Russ -Original Message- From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: Thursday, May 4, 2017 3:06 AM To: Lenth, Russell V <russell-le...@uiowa.edu>; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] Any new dev

[R-pkg-devel] Any new developments on "apparent S3 method" issue?

Package developers list: I recently added an 'as.mcmc.list' method for objects in one of my packages. Now, in doing an --as-cran check, I get this message: * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: as.mcmc.list See

Re: [R-pkg-devel] Relicense to GPL-3?

Permission of "all other copyright holders" as in developers of all packages that depend on 'foo'? Russ Sent from my iPhone > On Nov 6, 2016, at 9:31 AM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote: > >> On 06/11/2016 4:11 AM, Lenth, Russell V wrote: >&

Re: [R-pkg-devel] Relicense to GPL-3?

?) -- OR -- 2. The developer of 'bar' removes the dependency on 'foo', by not importing 'manchoo' or its S3method; instead, it simply exports the function 'manchoo.bar' and moves 'foo' to Suggests Thanks for any suggestions Russ -Original Message- From: Lenth, Russell V Sent: Saturday

[R-pkg-devel] Software ecosystems survey

Package developers, I am acquainted with one of the authors of an interesting article on how software developers respond to, and manage, evolutionary changes in various multi-developer computing "ecosystems". The article has some preliminary results based on interviews with small numbers of

Re: [R-pkg-devel] Absent variables and tibble

, potentially extensible to other classes. Thanks so much, several of you, for your positive and helpful responses. Russ -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: Monday, June 27, 2016 12:50 PM To: Hadley Wickham <h.wick...@gmail.com>; Lenth, Rus

Re: [R-pkg-devel] Absent variables and tibble

h.wick...@gmail.com> wrote: > > On Mon, Jun 27, 2016 at 9:03 AM, Duncan Murdoch > <murdoch.dun...@gmail.com> wrote: >> On 27/06/2016 9:22 AM, Lenth, Russell V wrote: >>> >>> My package 'lsmeans' is now suddenly broken because of a new provision in >>>

Re: [R-pkg-devel] Best practices for vignettes

office (319)335-0712 - FAX (319)335-3017 russell-le...@uiowa.edu - http://www.stat.uiowa.edu/~rlenth/ From: Henrik Bengtsson [henrik.bengts...@ucsf.edu] Sent: Monday, July 27, 2015 5:50 AM To: Lenth, Russell V Cc: Dirk Eddelbuettel; r-package-devel@r

Re: [R-pkg-devel] Best practices for vignettes

age, I think I am empowered to choose what I want to learn -- and expertise on Markdown is just not a big priority. Russ -Original Message- From: Dirk Eddelbuettel [mailto:e...@debian.org] Sent: Sunday, July 26, 2015 2:31 PM To: Dirk Eddelbuettel e...@debian.org Cc: Lenth, Russell V