Re: [R-pkg-devel] [R] a question of etiquette

Thanks for this information, Mark. Given the phrase "small but important function my package uses", it seems that you included in your package some code, reproducing it verbatim. Do I understand correctly? In my case, the code which I am actually using is the R porting of code originally writte

Re: [R-pkg-devel] [R] a question of etiquette

The point in question does not refer to copying code, but to code translation. Does this make any difference? This was the question which I raised. The phrase "As the code is part of the package now," does not seem to apply in this case, since the code is actually not there. Also, if the author

[R-pkg-devel] S4 methods

Dear members I just finished some minor updates to an R package (sizeMat) I've had on CRAN (haven't had to update in a month). My package passes Check on my local machine, but it just bounced back from CRAN with the message Warning: S4 exports specified in 'NAMESPACE' but not defined in package '

Re: [R-pkg-devel] S4 methods

This is a new check in R-devel. The NEWS say: > R CMD check etc now warn when a package exports non-existing S4 classes or > methods, also in case of no "methods" presence In your case, the NAMESPACE contains > exportClasses(classify) > exportClasses(gonad_mature) > exportClasses(morphMat) b

Re: [R-pkg-devel] S4 methods

You export these S4 classes from your package: https://github.com/cran/sizeMat/blob/c4d257a9108cde3ddb6e8eb2072cd567ae85b5c8/NAMESPACE#L13-L15 But these are not actually S4 classes, AFAICT. Remove the `@exportClass` tags here: https://github.com/cran/sizeMat/blob/c4d257a9108cde3ddb6e8eb2072cd567ae

Re: [R-pkg-devel] [R] a question of etiquette

To present a contrary view... To me the commentary so far doesn't seem right -- if I were writing an academic paper (I personally think this is a good analogy for many R packages) and elaborating on the ideas of someone else, I would cite their work but I would not add them as an author to my p

Re: [R-pkg-devel] [R] a question of etiquette

I had similar thoughts initially, but this area is governed by copyright, not academic authorship conventions. So (a) There is no real parallel to "citation rights" when it comes to software. If you use someone else's code, then it is very hard to avoid derived-works rules applying. (b) Copyr

[R-pkg-devel] win-builder failing without informative message

Hello List! I am prepping gtsummary for a new release, but I am running into a problem with the CRAN win-builder. The package is passing checks on my local Windows machine, another local Windows machine, on a GitHub Actions Windows machine ( https://github.com/ddsjoberg/gtsummary/runs/729569705?c

Re: [R-pkg-devel] win-builder failing without informative message

Seems like your tests did not finish: https://win-builder.r-project.org/SFSFeP44df58/examples_and_tests/tests_x64/testthat.Rout Either they take too long, or they froze. You can use a different testthat reporter, to see which one is stuck, e.g. like this: https://github.com/cran/desc/blob/3e52b492

Re: [R-pkg-devel] win-builder failing without informative message

In my opinion, if you've tested on multiple Windows system that you've done your due diligence and shouldn't worry too much about win-builder hiccups ... On Tue, Jun 2, 2020 at 10:09 AM Daniel Sjoberg wrote: > > Hello List! > > I am prepping gtsummary for a new release, but I am running into a

Re: [R-pkg-devel] [R] a question of etiquette

> Adelchi Azzalini > on Tue, 2 Jun 2020 08:32:37 +0200 writes: > Thanks for this information, Mark. Given the phrase > "small but important function my package uses", it seems > that you included in your package some code, reproducing > it verbatim. Do I understand c

Re: [R-pkg-devel] [R] a question of etiquette

On 2 June 2020 at 10:06, R. Mark Sharp wrote: | The GPL-2 and GPL-3 licenses are apparently sufficiently ambiguous in the legal community that some companies avoid them. Wittgenstein: 'That whereof we cannot speak, thereof we must remain silent' This is a mailing list of the R project. R is a

Re: [R-pkg-devel] [R] a question of etiquette

Thanks to all people that contributed to this discussion, which turned out to be interesting, definitely not something which I expected at the beginning. To avoid verbosity, I restrict myself to two more points. (1) In case one adopts the indication that all the authors of a portion of code (i

Re: [R-pkg-devel] [R] a question of etiquette

  Can Dr. Sharp kindly provide a credible reference, discussing the alleged ambiguities in GPL-2 and GPL-3 that convince some companies to avoid them?   I like Wikimedia Foundation projects like Wikipedia, where almost anyone can change almost anything, and what stays tends to be writ

Re: [R-pkg-devel] [R] a question of etiquette

On 02/06/2020 11:14 a.m., Adelchi Azzalini wrote: Thanks to all people that contributed to this discussion, which turned out to be interesting, definitely not something which I expected at the beginning. To avoid verbosity, I restrict myself to two more points. (1) In case one adopts the indi

Re: [R-pkg-devel] win-builder failing without informative message

Simply: ** running tests for arch 'i386' ... [14m] OK And the CRAN threshold for the whole package is 10 min. So only the tests for two architectures already take ~ 30 min here. which is too much for CRAN. Best, Uwe Ligges On 02.06.2020 16:13, Gábor Csárdi wrote: Seems like your tests d

Re: [R-pkg-devel] [R] a question of etiquette

On 2020-06-02 10:14, Adelchi Azzalini wrote: In general, "check the license" is a very sensible indication. In the specific case, the Matlab code comes with no licence indication - nothing.   I'm not an attorney, but it's my understanding that "no license indication" is a legal mi

Re: [R-pkg-devel] win-builder failing without informative message

Thank you! I added skip on CRAN to the time intensive tests, and it's passing again. MUCH APPRECIATED! On Tue, Jun 2, 2020 at 12:03 PM Uwe Ligges wrote: > Simply: > > ** running tests for arch 'i386' ... [14m] OK > > And the CRAN threshold for the whole package is 10 min. So only the > tests f

[R-pkg-devel] Including fonts in an rmarkdown vignette

Hi, I'd like to build a rmarkdown vignette with my own choice of fonts – I'm pernickety about look and feel. R CMD check will rebuild vignettes in the vignettes/ directory, and if relevant fonts aren't on the build machine, it'll give a warning. Here are the options I can think of: * build vigne

Re: [R-pkg-devel] [R] a question of etiquette

Adelchi, Actually, the person recognized wrote the original code for the algorithm and he has had other contributors over time that have made several improvements. The code I have is not verbatim from his package as it has been adapted for our purposes, but he is still the originator of the app

Re: [R-pkg-devel] [R] a question of etiquette

On Tue, Jun 2, 2020 at 5:04 PM Spencer Graves < spencer.gra...@effectivedefense.org> wrote: > QUESTION: How much money have people on this list received for what > they've written? I've received not one penny for any technical article > I've written or for software contributed to CRAN. > >

[R-pkg-devel] Vignette depends on BH

I have an RMarkdown vignette in a package that uses Rcpp and depends on BH. I added BH to the Suggests list. It is still generating warnings about BH. What is the correct way to handle this? Thanks. THK [[alternative HTML version deleted]] __

Re: [R-pkg-devel] Vignette depends on BH

On 02/06/2020 3:45 p.m., Tim Keitt wrote: I have an RMarkdown vignette in a package that uses Rcpp and depends on BH. I added BH to the Suggests list. It is still generating warnings about BH. What is the correct way to handle this? If a package is listed in Suggests, it should still work (poss

Re: [R-pkg-devel] [R] a question of etiquette

On 2020-06-02 14:24, Avraham Adler wrote: > > > On Tue, Jun 2, 2020 at 5:04 PM Spencer Graves > > wrote: > > QUESTION:  How much money have people on this list received for what > > they've written?  I've received not one penny for any technical art

Re: [R-pkg-devel] [R] a question of etiquette

For academics, aren't those citations the currency in which they are supposed to be paid (at least for R packages)?   Kevin On 6/2/2020 3:24 PM, Avraham Adler wrote: On Tue, Jun 2, 2020 at 5:04 PM Spencer Graves < spencer.gra...@effectivedefense.org> wrote: QUESTION: How much money have peo

Re: [R-pkg-devel] S4 methods

Thank you so much for your help. I delete the exporClass and the warnings and error have disappeared. Regards El mar., 2 jun. 2020 a las 4:28, Gábor Csárdi () escribió: > You export these S4 classes from your package: > > https://github.com/cran/sizeMat/blob/c4d257a9108cde3ddb6e8eb2072cd567ae85

Re: [R-pkg-devel] [R] a question of etiquette

IANAL, but the GPL family of licenses is VIRAL copy left so it infects anything it touched, which is why many shy away and prefer something like the Mozilla Public License 2 (MPL) as a compromise between viral copyleft and the permissive MIT/ISC/BSD2. Avi On Tue, Jun 2, 2020 at 7:32 PM R. Mark Sh

Re: [R-pkg-devel] [R] a question of etiquette

On 2 June 2020 at 18:32, R. Mark Sharp wrote: | I apologize for my obvious (in hindsight) error in bringing up the topic. I will bring up one example, because of your request. Google has listed GPL-1, 2, and 3 as one of several licenses that are restricted and cannot be used by a Google produc

Re: [R-pkg-devel] [R] a question of etiquette

"Viral" is has connotations that reflect the biases of the person using the term. A less loaded perspective is that some people don't want you to take their contributions out of circulation by using it as the foundation of your proprietary work. If you want to close it up, build from scratch or

Re: [R-pkg-devel] [R] a question of etiquette

Apologies; my intent was not to disparage, but that is the term is used in the industry and in venues which discuss FLOSS because it reflects that the addition of one component with that kind of copyleft license causes the entire project to need that particular copyleft license. If there is a term

Re: [R-pkg-devel] [R] a question of etiquette

The obvious answer is simply to refer to GPL. It isn't necessary to propagate a derogatory point of view by finding another word for an incorrect idea. Try re-reading my previous words without trying to hold on to a flawed interpretation. On June 2, 2020 5:33:56 PM PDT, Avraham Adler wrote: >

Re: [R-pkg-devel] [R] a question of etiquette

I respectfully submit that the mechanism is accurately described as “viral” albeit the connotations may be uncomfortable. I will refrain from commenting further in this thread. Happy to continue with you off-list if you wish. Thank you, Aavi On Tue, Jun 2, 2020 at 8:43 PM Jeff Newmiller wrote:

Re: [R-pkg-devel] [R] a question of etiquette

Spencer, I apologize for my obvious (in hindsight) error in bringing up the topic. I will bring up one example, because of your request. Google has listed GPL-1, 2, and 3 as one of several licenses that are restricted and cannot be used by a Google product delivered to outside customers. This i

Re: [R-pkg-devel] [R] a question of etiquette

On Tue, 2 Jun 2020 20:33:56 -0400 Avraham Adler wrote: > If there is a term which reflects that mechanism from a discipline > other than biology, please let me know. I think that "copyleft" is the term you are looking for. The Wikipedia page [*] defines it as >> the practice of offering people