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

[Martin Maechler]

> Lenth, Russell V 
> on Tue, 21 Sep 2021 18:43:07 + writes:

> As I suspected, and a good point. But please note that the term "retired" 
causes angst, and it may be good to change that to "superceded" or something 
else.

well,  some of us will  become "retired" somewhere in the
future rather than "superseded" .. ;-)

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

[Spencer Graves]

On 9/22/21 2:38 AM, Martin Maechler wrote:

Lenth, Russell V
 on Tue, 21 Sep 2021 18:43:07 + writes:


 > As I suspected, and a good point. But please note that the term "retired" causes 
angst, and it may be good to change that to "superceded" or something else.

well,  some of us will  become "retired" somewhere in the
future rather than "superseded" .. ;-)



yes, but we'll become "superseded" long before we want to admit it ;-)



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

[Avi Gross via R-package-devel]

Philosophy aside, albeit not uninteresting, I am wondering about the
etiquette of developing a package and then years later dealing with how to
have it replaced carefully. Do creators and maintainers have any obligation
and especially when there is a large remaining embedded base of users. We
may have quite a few Y2K type problems in the sense that some people cannot
easily change what is being used. Other languages, like Python, have been
dealing with how the newer language features (version 3) have serious
incompatibilities with earlier versions and yet some stay with what they
have.

Hadley Wickham for example, has been involved in multiple packages including
cases like ggplot where it was replaced by another package with enough
incompatibilities that it might merit another name. I am not sure what
exactly was in plyr when it stopped being changed but in some ways the dplyr
package seems to focus on data.frames and plyr was more general. And, I
suspect, dplyr also tried to do things consistent with new design approaches
such as standardizing where arguments to a function go. It may well be
faster when used as planned.

But as a possibility, I suspect you could theoretically take the source code
for a package that has largely been replaced by others and sometimes make a
sort of compatibility version that consists largely of pointers to other
packages.

Specifically, the documentation could contain a section that suggests
alternatives to use. I suspect quite a few of the included functions may be
available in base R or another commonly used package (such as the tidyverse
collection) and just using the new one, perhaps with some alteration in how
it is called, might help guide existing users away to something more likely
to be maintained.

And sometimes, it might be weirdly possible to have a volunteer do something
a tad odd and set up a way to replace the functions in the package. A
function call like f(z, data) might simply be mapped into a call to
other::g(data, z, flag=FALSE) if that made sense. Other fairly small
wrappers might do more such re-direction. Obviously, this would be of
limited use if other packages would need to be loaded. I can imagine leaving
a package intact and adding a new function with a name like supercede() that
would make such a re-arrangement when asked to.

The user would normally call:

library(plyr)
plyr::supercede()

Without that additional line, nothing changes. But after calling it, you may
now be in a partial compatibility mode.

I now retire without being superseded.

-Original Message-
From: R-package-devel  On Behalf Of
Martin Maechler
Sent: Wednesday, September 22, 2021 3:39 AM
To: Lenth, Russell V 
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] [External] Re: What is a "retired"package?

> Lenth, Russell V 
> on Tue, 21 Sep 2021 18:43:07 + writes:

> As I suspected, and a good point. But please note that the term
"retired" causes angst, and it may be good to change that to "superceded" or
something else.

well,  some of us will  become "retired" somewhere in the future rather than
"superseded" .. ;-)

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Re: [R-pkg-devel] README.html doesn't show figures in CRAN web

[Jose Barrera]

Dear Duncan,

Indeed, I had accidentally deleted man/figures before tar.gz. Silly error.
Now fixed and working. Thanks for the light.

Jose Barrera
Statistician, Associate Lecturer

ISGlobal
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research Park (PRBB) (Room Hypatia)

Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 2147383
jose.barr...@isglobal.org
www.isglobal.org


El lun., 20 sept. 2021 19:04, Duncan Murdoch 
escribió:

> On 20/09/2021 12:37 p.m., Jose Barrera wrote:
> > Hi everyone,
> >
> > I have a package at CRAN that includes a README.html which includes two
> > figures created by two R chunks in the README.Rmd. Once the package were
> at
> > CRAN, I noticed that
> > https://cran.r-project.org/web/packages/mypkg/readme/README.html doesn't
> > show the figures. Instead, the usual icon of image not found is
> displayed.
>
> The rgl package does something similar to you, though it includes the
> .md file instead of the .html.  The output spec is
>
> output: github_document
>
> CRAN processes the .md to produce the display properly.  This also works
> on Github.
>
> You do need to make sure the man/figures directory is included in the
> tarball.  Check your .Rbuildignore file for patterns that might exclude it.
>
> Duncan Murdoch
>
> >
> > Locally, README.html works fine (both figures are shown). I think the
> > problem could be that
> > https://cran.r-project.org/web/packages/mypkg/readme/README.html doesn't
> > find the figure files because I possibly put them in a wrong folder.
> >
> > In my Rmd, I set
> >
> > knitr::opts_chunk$set(fig.path = "man/figures/README-")
> >
> > I can see the folder "figures" is created in "man" but, "figures" folder
> is
> > not in the tar.gz. I didn't notice that before because I didn't get any
> > warning nor note.
> >
> > In "R packages", section 20.5.2, I can see, they set
> >
> > knitr::opts_chunk$set(fig.path = "README-)
> >
> > Should I set fig.path = "README-" instead of fig.path =
> > "man/figures/README-" even if my html is not for GitHub? Where should I
> > place the png figure files created by the Rmd?
> >
> > Any thoughts would be greatly appreciated.
> >
> > Thanks,
> >
> > Jose Barrera
> > Statistician, Associate Lecturer
> >
> > *IS**Global*
> > Barcelona Institute for Global Health - Campus MAR
> > Barcelona Biomedical Research Park (PRBB) (Room Hypatia)
> >
> > Doctor Aiguader, 88
> > 08003 Barcelona, Spain
> > Tel. +34 93 2147383
> > jose.barr...@isglobal.org
> > 
> > Personal website: sites.google.com/view/josebarrera
> > www.isglobal.org
> >
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This 

[R-pkg-devel] ERROR (re)building vignettes

[Blume Christine]

Dear community,

When building my package 'SleepCycles' using devtools::check, 
devtools::check_win_devel, and devtools::check_rhub, I do not get warnings, 
errors, or notes. Nevertheless, there seems to be an error when building the 
vignettes eventually 
(https://cran-archive.r-project.org/web/checks/2021/2021-09-06_check_results_SleepCycles.html),
 which I did not notice and which led to the removal of the package.

Does anyone know how to solve this? I read something about changing the 
vignette engine, but when I tried this, I ran into other issues.

I cannot replicate the error, but simply resubmitting will most likely result 
in the same issue again.

Best,
Christine


[[alternative HTML version deleted]]

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Re: [R-pkg-devel] ERROR (re)building vignettes

[Maëlle SALMON via R-package-devel]

Dear Christine,

Looking at the chunk that causes the error 
https://github.com/cran/SleepCycles/blob/141186934418af387f0af257e3079af588e72844/vignettes/introduction.Rmd#L50-L56
 (via the CRAN mirror maintained by R-hub):

* You should not install packages from a vignette. You can add "eval=FALSE" as 
a chunk option.
* Regarding the other lines in that chunk, they do not provoke an error but are 
not recommended by all. See e.g. 
https://www.tidyverse.org/blog/2017/12/workflow-vs-script/

Good luck with re-submission!

Maëlle.




Den onsdag 22 september 2021 22:20:36 CEST, Blume Christine 
 skrev: 





Dear community,

When building my package 'SleepCycles' using devtools::check, 
devtools::check_win_devel, and devtools::check_rhub, I do not get warnings, 
errors, or notes. Nevertheless, there seems to be an error when building the 
vignettes eventually 
(https://cran-archive.r-project.org/web/checks/2021/2021-09-06_check_results_SleepCycles.html),
 which I did not notice and which led to the removal of the package.

Does anyone know how to solve this? I read something about changing the 
vignette engine, but when I tried this, I ran into other issues.

I cannot replicate the error, but simply resubmitting will most likely result 
in the same issue again.

Best,
Christine


    [[alternative HTML version deleted]]

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