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

ke me less 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,

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! __ R-package-devel@r-project.or

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 -> update.emmGrid.

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

12:22 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

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

comp::cld(). It just 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] Doc

[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 o

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

Mod" Using the setup that Luke suggests, I have a default_recover_data.stanreg() method, but it is not used because it finds the lm method instead of going to recover_data.default. Russ -Original Message- From: Tierney, Luke Sent: Saturday, August 10, 2019 3:15 PM To: Lenth, Russel

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

Sent: Saturday, 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 d

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

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

egister()' 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-packag

[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 cre

Re: [R-pkg-devel] [External] Re: pandoc version used in winbuilder

To: Lenth, Russell V ; r-package-devel@r-project.org Subject: [External] Re: [R-pkg-devel] pandoc version used in winbuilder On 27/06/2019 9:51 a.m., Duncan Murdoch wrote: > On 26/06/2019 2:54 p.m., Lenth, Russell V wrote: >> All, >> >> How does one tell what version of pandoc i

[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 ha

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

g 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

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, Ju

[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 t

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 Cc: r-pac

[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 to

[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 bu

[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 like

[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 t

[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 S3

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

at such a check-exclusion-inheritance provision 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 ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel

[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 se

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 wrote: > >> On 06/11/2016 4:11 AM, Lenth, Russell V wrote: >> A correction and clar

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

1. The developer of 'foo' changes its license to GPL-3 (does that indeed resolve the license issue?) -- OR -- 2. The developer of 'bar' removes the dependency on 'foo', by not importing 'manchoo' or its S3method; instead, it simply exports the function &#x

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

Dear all, I received an email from a user telling me that another package that depends on my package is licensed GPL(>=3), whereas mine is licensed GPL-2; and that therefore, the other package is in violation of its GPL-3 license. This apparently causes an issue with the Debian packaging system

[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 dev

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

ibute, 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 ; Lenth, Russell V Cc: r-package-de

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

Wickham wrote: > > On Mon, Jun 27, 2016 at 9:03 AM, Duncan Murdoch > 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 >>> the 'tibble' package

[R-pkg-devel] Absent variables and tibble

My package 'lsmeans' is now suddenly broken because of a new provision in the 'tibble' package (loaded by 'dplyr' 0.5.0), whereby the "[[" and "$" methods for 'tbl_df' objects - as documented - throw an error if a variable is not found. The problem is that my code uses tests like this:

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

52242 USA Dept 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-

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

w things, but at my 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 Cc: Lenth, Russell

[R-pkg-devel] Best practices for vignettes

Yesterday, I submitted a package to CRAN that I had previously built using `R CMD build' (no extra arguments), and checked with 'R-devel CMD check --as-cran' (R-devel is my installation of the latest development version). No errors were reported in either of these steps. However, the submitted