date:20240103

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

2024-01-03 Thread Daniel Kelley

Answering my own question here ...

The problem was that I was using

mooringS7 <- S7::new_class("mooring", ETC

instead of

mooringS7 <- S7::new_class("mooringS7", ETC

With the change to the latter, all works fine now.  Thanks very much to all who 
have helped, so generously and so quickly.  

I wish a very Happy New Year, to all!!

Dan.

Dan Kelley / Oceanography Department / Dalhousie University / Halifax, Nova 
Scotia / Canada


> On Jan 3, 2024, at 3:18 PM, Daniel Kelley  wrote:
> 
> Oh, Hadley, I'm sorry to bother you whilst you're on vacation.  Please don't 
> take too much time on.  I'm certainly not in a rush at all.
> 
> To answer your question, yes, I rebuilt the documentation (within RStudio, 
> via the 'More/Document' scheme) and it still fails.
> 
> I wonder if I need to do a
> 
> method(plot, mooring:::mooringS7) <- function(ETC) {ETC}
> 
> instead of
> 
> `plot.mooring::mooring` <- function(ETC) {ETC}
> 
> which is what I'm doing now, and which works for plotting but not 
> webpage-building.
> 
> PS. That `mooringS7` vs `mooring` name difference is because I am using
> 
> mooringS7 <- S7::new_class("mooring", ETC
> 
> because I want the user-facing function to be called `mooring`.  (I am having 
> the user using the object constructor directly.  I guess I could, but I'm 
> doing it this way to retain my old code, which used S3 methodology and had a 
> fair bit of logic before constructing a return value.  I can change that, of 
> course.  For now, my S7 steps are a bit timid, so I can fall back to my S3 
> code if I cannot figure things out.)
> 
> 
> 
> On Jan 3, 2024, at 2:48 PM, Hadley Wickham  wrote:
> 
> CAUTION: The Sender of this email is not from within Dalhousie.
> Did you re-document? You’ll need that to correctly regenerate the .Rd, I 
> think. (Sorry I’m on vacation so I’m guessing at stuff from my phone)
> 
> Hadley
> 
> On Thursday, January 4, 2024, Daniel Kelley 
> mailto:kel...@dal.ca>> wrote:
> Thanks.  I installed the latest roxygen2 and pkgdown, and tried to make a 
> simple reprex
> git clone https://github.com/dankelley/mooring.git
> cd mooring
> git checkout S7
> Rscript -e "pkgdown::clean_site()"
> Rscript -e "pkgdown::build_site()"
> 
> but it still fails.  (Full output is below, for completeness.) I wonder 
> whether I ought to be doing something extra in the Roxygen code (in file 
> R/plot.R within this directory.). Please note that I can rename it as 
> "draw()" or something, but I'm hoping to learn S7 properly, because I'm 
> really quite keen to leave my S3 and S4 days behind me.  (PS to Hadley: I 
> loved the presentation you gave on what was then R7, and have recommended it 
> to colleagues not just for the R7 information, but for the concise 
> explanation of the benefit of OOP and generics.)
> 
> ── Installing package mooring into temporary library 
> ───
> ── Building pkgdown site for package mooring 
> ───
> Reading from: /Users/kelley/wednesday/mooring
> Writing to: /Users/kelley/wednesday/mooring/docs
> ── Initialising site 
> ───
> Copying
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.css,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.js,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.css,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.js,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/link.svg,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/pkgdown.css,
> and
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/pkgdown.js
> to bootstrap-toc.css, bootstrap-toc.js, docsearch.css, docsearch.js, link.svg,
> pkgdown.css, and pkgdown.js
> ── Building home 
> ───
> Writing authors.html
> Copying man/figures/Makefile, man/figures/README-example-1.png,
> man/figures/README-example-2.png, man/figures/force_diagram.R, and
> man/figures/force_diagram.png
> to reference/figures/Makefile, reference/figures/README-example-1.png,
> reference/figures/README-example-2.png, reference/figures/force_diagram.R, and
> reference/figures/force_diagram.png
> Writing 404.html
> ── Building function reference 
> ─
> Error:
> ! in callr subprocess.
> Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
> ! In index: 1.
> ---
> Standard error:
> ── Building pkgdown site for package mooring 
> ───
> Reading from: /Users/kelley/wednesday/mooring
> Writing to: /Users/kelley/wednesday/mooring/docs
>

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

2024-01-03 Thread Daniel Kelley

Oh, Hadley, I'm sorry to bother you whilst you're on vacation.  Please don't 
take too much time on.  I'm certainly not in a rush at all.

To answer your question, yes, I rebuilt the documentation (within RStudio, via 
the 'More/Document' scheme) and it still fails.

I wonder if I need to do a

method(plot, mooring:::mooringS7) <- function(ETC) {ETC}

instead of

`plot.mooring::mooring` <- function(ETC) {ETC}

which is what I'm doing now, and which works for plotting but not 
webpage-building.

PS. That `mooringS7` vs `mooring` name difference is because I am using

mooringS7 <- S7::new_class("mooring", ETC

because I want the user-facing function to be called `mooring`.  (I am having 
the user using the object constructor directly.  I guess I could, but I'm doing 
it this way to retain my old code, which used S3 methodology and had a fair bit 
of logic before constructing a return value.  I can change that, of course.  
For now, my S7 steps are a bit timid, so I can fall back to my S3 code if I 
cannot figure things out.)



On Jan 3, 2024, at 2:48 PM, Hadley Wickham  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Did you re-document? You’ll need that to correctly regenerate the .Rd, I think. 
(Sorry I’m on vacation so I’m guessing at stuff from my phone)

Hadley

On Thursday, January 4, 2024, Daniel Kelley 
mailto:kel...@dal.ca>> wrote:
Thanks.  I installed the latest roxygen2 and pkgdown, and tried to make a 
simple reprex
git clone https://github.com/dankelley/mooring.git
cd mooring
git checkout S7
Rscript -e "pkgdown::clean_site()"
Rscript -e "pkgdown::build_site()"

but it still fails.  (Full output is below, for completeness.) I wonder whether 
I ought to be doing something extra in the Roxygen code (in file R/plot.R 
within this directory.). Please note that I can rename it as "draw()" or 
something, but I'm hoping to learn S7 properly, because I'm really quite keen 
to leave my S3 and S4 days behind me.  (PS to Hadley: I loved the presentation 
you gave on what was then R7, and have recommended it to colleagues not just 
for the R7 information, but for the concise explanation of the benefit of OOP 
and generics.)

── Installing package mooring into temporary library ───
── Building pkgdown site for package mooring ───
Reading from: /Users/kelley/wednesday/mooring
Writing to: /Users/kelley/wednesday/mooring/docs
── Initialising site ───
Copying
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.css,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.js,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.css,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.js,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/link.svg,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/pkgdown.css,
and
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/pkgdown.js
to bootstrap-toc.css, bootstrap-toc.js, docsearch.css, docsearch.js, link.svg,
pkgdown.css, and pkgdown.js
── Building home ───
Writing authors.html
Copying man/figures/Makefile, man/figures/README-example-1.png,
man/figures/README-example-2.png, man/figures/force_diagram.R, and
man/figures/force_diagram.png
to reference/figures/Makefile, reference/figures/README-example-1.png,
reference/figures/README-example-2.png, reference/figures/force_diagram.R, and
reference/figures/force_diagram.png
Writing 404.html
── Building function reference ─
Error:
! in callr subprocess.
Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
! In index: 1.
---
Standard error:
── Building pkgdown site for package mooring ───
Reading from: /Users/kelley/wednesday/mooring
Writing to: /Users/kelley/wednesday/mooring/docs
── Initialising site ───
Copying
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.css,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.js,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.css,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.js,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/link.svg,
../../../../Library/Frameworks/R.framework/Versi

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

2024-01-03 Thread Hadley Wickham

Did you re-document? You’ll need that to correctly regenerate the .Rd, I
think. (Sorry I’m on vacation so I’m guessing at stuff from my phone)

Hadley

On Thursday, January 4, 2024, Daniel Kelley  wrote:

> Thanks.  I installed the latest roxygen2 and pkgdown, and tried to make a
> simple reprex
> git clone https://github.com/dankelley/mooring.git
> cd mooring
> git checkout S7
> Rscript -e "pkgdown::clean_site()"
> Rscript -e "pkgdown::build_site()"
>
> but it still fails.  (Full output is below, for completeness.) I wonder
> whether I ought to be doing something extra in the Roxygen code (in file
> R/plot.R within this directory.). Please note that I can rename it as
> "draw()" or something, but I'm hoping to learn S7 properly, because I'm
> really quite keen to leave my S3 and S4 days behind me.  (PS to Hadley: I
> loved the presentation you gave on what was then R7, and have recommended
> it to colleagues not just for the R7 information, but for the concise
> explanation of the benefit of OOP and generics.)
>
> ── Installing package mooring into temporary library
> ───
> ── Building pkgdown site for package mooring ──
> ─
> Reading from: /Users/kelley/wednesday/mooring
> Writing to: /Users/kelley/wednesday/mooring/docs
> ── Initialising site ──
> ─
> Copying
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/bootstrap-toc.css,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/bootstrap-toc.js,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/docsearch.css,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/docsearch.js,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/link.svg,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/pkgdown.css,
> and
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/pkgdown.js
> to bootstrap-toc.css, bootstrap-toc.js, docsearch.css, docsearch.js,
> link.svg,
> pkgdown.css, and pkgdown.js
> ── Building home ──
> ─
> Writing authors.html
> Copying man/figures/Makefile, man/figures/README-example-1.png,
> man/figures/README-example-2.png, man/figures/force_diagram.R, and
> man/figures/force_diagram.png
> to reference/figures/Makefile, reference/figures/README-example-1.png,
> reference/figures/README-example-2.png, reference/figures/force_diagram.R,
> and
> reference/figures/force_diagram.png
> Writing 404.html
> ── Building function reference ──
> ───
> Error:
> ! in callr subprocess.
> Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
> ! In index: 1.
> ---
> Standard error:
> ── Building pkgdown site for package mooring ──
> ─
> Reading from: /Users/kelley/wednesday/mooring
> Writing to: /Users/kelley/wednesday/mooring/docs
> ── Initialising site ──
> ─
> Copying
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/bootstrap-toc.css,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/bootstrap-toc.js,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/docsearch.css,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/docsearch.js,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/link.svg,
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/pkgdown.css,
> and
> ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/
> library/pkgdown/BS3/assets/pkgdown.js
> to bootstrap-toc.css, bootstrap-toc.js, docsearch.css, docsearch.js,
> link.svg,
> pkgdown.css, and pkgdown.js
> ── Building home ──
> ─
> Writing authors.html
> Copying man/figures/Makefile, man/figures/README-example-1.png,
> man/figures/README-example-2.png, man/figures/force_diagram.R, and
> man/figures/force_diagram.png
> to reference/figures/Makefile, reference/figures/README-example-1.png,
> reference/figures/README-example-2.png, reference/figures/force_diagram.R,
> and
> reference/figures/force_diagram.png
> Writing 404.html
> ── Building function reference ──
> ───
> ---
> Backtrace:
> 1. pkgdown::build_site()
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples,
> run_dont_run = run

Re: [R-pkg-devel] Suggests with non-CRAN packages

2024-01-03 Thread Uwe Ligges

From the CRAN polcies:

"Packages on which a CRAN package depends should be available from a 
mainstream repository: if any mentioned in ‘Suggests’ or ‘Enhances’ 
fields are not from such a repository, where to obtain them at a 
repository should be specified in an ‘Additional_repositories’ field of 
the DESCRIPTION file (as a comma-separated list of repository URLs) or 
for other means of access, described in the ‘Description’ field. "

Best,
Uwe Ligges

On 03.01.2024 18:19, Josiah Parry wrote:
Thanks, both. I'm not familiar with Additional_repositories. Must the 
package source be specified there? Or can it be specified via 
documentation a la Rd file?

On Wed, Jan 3, 2024 at 12:14 PM Uwe Ligges 
> wrote:

On 03.01.2024 17:58, Duncan Murdoch wrote:
 > On 03/01/2024 11:33 a.m., Josiah Parry wrote:
 >> I have a scenario where I have an exported function that
requires the
 >> installation a package that *is not* available on CRAN. The body
of the
 >> function is generally:
 >>
 >> fx <- function() {
 >>    rlang::check_installed("noncranpkg")
 >>    noncranpkg::gx()
 >> }
 >>
 >> As required, this package is in the Suggests field. But this
results in a
 >> note:
 >>
 >> checking package dependencies ... NOTE
 >> Package suggested but not available for checking: ‘noncranpkg’
 >>
 >> Can this be safely ignored?
 >
 > Uwe said yes, and he's an authority.  But for your users, it
might be
 > nice to include an Additional_repositories field so they can find
the
 > package.  This needs to be organized as an actual repository; the
drat
 > package is a very convenient way to set one up.

Thanks for elaborating, yes of course, people have to declare where to
get the package from. The note from above is still unavoidable in
that case.

Best,
Uwe

 >
 > Duncan Murdoch
 >
 > __
 > R-package-devel@r-project.org
 mailing list
 > https://stat.ethz.ch/mailman/listinfo/r-package-devel

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

2024-01-03 Thread Daniel Kelley

Thanks.  I installed the latest roxygen2 and pkgdown, and tried to make a 
simple reprex
git clone https://github.com/dankelley/mooring.git
cd mooring
git checkout S7
Rscript -e "pkgdown::clean_site()"
Rscript -e "pkgdown::build_site()"

but it still fails.  (Full output is below, for completeness.) I wonder whether 
I ought to be doing something extra in the Roxygen code (in file R/plot.R 
within this directory.). Please note that I can rename it as "draw()" or 
something, but I'm hoping to learn S7 properly, because I'm really quite keen 
to leave my S3 and S4 days behind me.  (PS to Hadley: I loved the presentation 
you gave on what was then R7, and have recommended it to colleagues not just 
for the R7 information, but for the concise explanation of the benefit of OOP 
and generics.)

── Installing package mooring into temporary library ───
── Building pkgdown site for package mooring ───
Reading from: /Users/kelley/wednesday/mooring
Writing to: /Users/kelley/wednesday/mooring/docs
── Initialising site ───
Copying
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.css,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.js,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.css,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.js,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/link.svg,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/pkgdown.css,
and
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/pkgdown.js
to bootstrap-toc.css, bootstrap-toc.js, docsearch.css, docsearch.js, link.svg,
pkgdown.css, and pkgdown.js
── Building home ───
Writing authors.html
Copying man/figures/Makefile, man/figures/README-example-1.png,
man/figures/README-example-2.png, man/figures/force_diagram.R, and
man/figures/force_diagram.png
to reference/figures/Makefile, reference/figures/README-example-1.png,
reference/figures/README-example-2.png, reference/figures/force_diagram.R, and
reference/figures/force_diagram.png
Writing 404.html
── Building function reference ─
Error:
! in callr subprocess.
Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
! In index: 1.
---
Standard error:
── Building pkgdown site for package mooring ───
Reading from: /Users/kelley/wednesday/mooring
Writing to: /Users/kelley/wednesday/mooring/docs
── Initialising site ───
Copying
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.css,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/bootstrap-toc.js,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.css,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/docsearch.js,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/link.svg,
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/pkgdown.css,
and
../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pkgdown/BS3/assets/pkgdown.js
to bootstrap-toc.css, bootstrap-toc.js, docsearch.css, docsearch.js, link.svg,
pkgdown.css, and pkgdown.js
── Building home ───
Writing authors.html
Copying man/figures/Makefile, man/figures/README-example-1.png,
man/figures/README-example-2.png, man/figures/force_diagram.R, and
man/figures/force_diagram.png
to reference/figures/Makefile, reference/figures/README-example-1.png,
reference/figures/README-example-2.png, reference/figures/force_diagram.R, and
reference/figures/force_diagram.png
Writing 404.html
── Building function reference ─
---
Backtrace:
1. pkgdown::build_site()
2. pkgdown:::build_site_external(pkg = pkg, examples = examples, run_dont_run = 
run_don…
3. callr::r(function(..., cli_colors, pkgdown_internet) { …
4. callr:::get_result(output = out, options)
5. callr:::throw(callr_remote_error(remerr, output), parent = 
fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. pkgdown::build_site(...)
 2. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_dont_run = 
run_dont_r…
 3. pkgdown::build_reference(pkg, lazy = lazy, examples = examples, 
run_dont_run = ru

Re: [R-pkg-devel] Suggests with non-CRAN packages

2024-01-03 Thread Josiah Parry

Thanks, both. I'm not familiar with Additional_repositories. Must the
package source be specified there? Or can it be specified via documentation
a la Rd file?

On Wed, Jan 3, 2024 at 12:14 PM Uwe Ligges 
wrote:

>
>
> On 03.01.2024 17:58, Duncan Murdoch wrote:
> > On 03/01/2024 11:33 a.m., Josiah Parry wrote:
> >> I have a scenario where I have an exported function that requires the
> >> installation a package that *is not* available on CRAN. The body of the
> >> function is generally:
> >>
> >> fx <- function() {
> >>rlang::check_installed("noncranpkg")
> >>noncranpkg::gx()
> >> }
> >>
> >> As required, this package is in the Suggests field. But this results in
> a
> >> note:
> >>
> >> checking package dependencies ... NOTE
> >> Package suggested but not available for checking: ‘noncranpkg’
> >>
> >> Can this be safely ignored?
> >
> > Uwe said yes, and he's an authority.  But for your users, it might be
> > nice to include an Additional_repositories field so they can find the
> > package.  This needs to be organized as an actual repository; the drat
> > package is a very convenient way to set one up.
>
> Thanks for elaborating, yes of course, people have to declare where to
> get the package from. The note from above is still unavoidable in that
> case.
>
> Best,
> Uwe
>
> >
> > Duncan Murdoch
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Suggests with non-CRAN packages

2024-01-03 Thread Uwe Ligges




On 03.01.2024 17:58, Duncan Murdoch wrote:

On 03/01/2024 11:33 a.m., Josiah Parry wrote:

I have a scenario where I have an exported function that requires the
installation a package that *is not* available on CRAN. The body of the
function is generally:

fx <- function() {
   rlang::check_installed("noncranpkg")
   noncranpkg::gx()
}

As required, this package is in the Suggests field. But this results in a
note:

checking package dependencies ... NOTE
Package suggested but not available for checking: ‘noncranpkg’

Can this be safely ignored?


Uwe said yes, and he's an authority.  But for your users, it might be 
nice to include an Additional_repositories field so they can find the 
package.  This needs to be organized as an actual repository; the drat 
package is a very convenient way to set one up.


Thanks for elaborating, yes of course, people have to declare where to 
get the package from. The note from above is still unavoidable in that case.


Best,
Uwe



Duncan Murdoch

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Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

2024-01-03 Thread Hadley Wickham

This bug is fixed in the dev version (I don’t remember off the top of my
head in which of pkgdown and roxygen2 you need but it might be both). I’m
planning CRAN updates for both in the near future.

Hadley

On Thursday, January 4, 2024, Daniel Kelley  wrote:

> # Question
>
> Is there an online example online of specializing `plot()` for S7 objects,
> such that `pkgdown::build_site()` will produce webpages?  I ask because I
> find lots of users (of other packages) tend to consult websites made with
> pkgdown, rather than using the online help within R.  I think the problem I
> am having (discussed in the following sections) has to do with my
> specialization of plot().  I say that because when I was using S3 objects
> in an earlier version of my package, `pkgdown::build_site()` worked as
> intended.
>
> # Background
>
> In my 'mooring' package (https://github.com/dankelley/mooring/tree/S7), I
> am writing code like (https://github.com/dankelley/mooring/blob/
> f70b53ca12e88968f65710c205b50a64f750a99d/R/plot.R#L69)
>
> ```R
> #' @aliases plot.mooring
> #' ETC
> `plot.mooring::mooring` <- plot(ETC) ETC
> ```
>
> to handle objects made with (https://github.com/dankelley/mooring/blob/
> f70b53ca12e88968f65710c205b50a64f750a99d/R/oo.R#L2)
>
> ```R
> mooringS7 <- S7::new_class("mooring",
> package = "mooring",
> ETC
> ```
>
> Built up in Rstudio, with Roxygen2 being used to create documentation,
> things seem to work, e.g.
>
> ```R
> m <- mooring(anchor(), wire(length = 80), float(), waterDepth = 100)
> plot(m)
> ```
>
> produces a plot as intended, and
>
> ```R
> ?plot.mooring
> ```
>
> produces documentation as intended.
>
> *However* I encounter a problem comes when I try building a website with
>
> ```R
> pkgdown::build_site()
> ```
>
> This yields results as in the next section.  (I apologize for the length.
> I'm including the whole thing because I thought that would be less
> bothersome than writing another email to the list.)
>
> I am not sure how to find the problem, and so I hope that someone on this
> list can point out an example of how to set up `plot()` to work with S7
> objects, in such a way that documentation can be created with Roxygen2 and
> websites can be made with `pkgdown::build_site()`.
>
> # What pkgdown::build_site() gives
>
> ```
> > library(pkgdown)
> > build_site()
> Warning: Failed to parse usage:
>
> S3method(`plot`, ``mooring::mooring``)(
>   x,
>   which = "shape",
>   showInterfaces = TRUE,
>   showDepths = FALSE,
>   showLabels = TRUE,
>   showDetails = FALSE,
>   fancy = FALSE,
>   title = "",
>   mar = c(1.5, 3.5, 3.5, 1),
>   mgp = c(2, 0.7, 0),
>   xlim = NULL,
>   xaxs = "r",
>   yaxs = "r",
>   type = "l",
>   debug = 0,
>   ...
> )
>
> -- Installing package into temporary library 
> == Building pkgdown site ==
> =
> Reading from: '/Users/kelley/git/mooring'
> Writing to:   '/Users/kelley/git/mooring/docs'
> -- Initialising site --
> -
> -- Building home --
> -
> Writing '404.html'
> -- Building function reference --
> ---
> Error:
> ! in callr subprocess.
> Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
> ! In index: 1.
> ℹ See `$stdout` for standard output.
> Type .Last.error to see the more details.
> > .Last.error
> 
> Error:
> ! in callr subprocess.
> Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
> ! In index: 1.
> ℹ See `$stdout` for standard output.
> ---
> Backtrace:
> 1. pkgdown::build_site()
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, run…
> 3. callr::r(function(..., cli_colors, pkgdown_internet) { …
> 4. callr:::get_result(output = out, options)
> 5. callr:::throw(callr_remote_error(remerr, output), parent = fix_…
> ---
> Subprocess backtrace:
>  1. pkgdown::build_site(...)
>  2. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do…
>  3. pkgdown::build_reference(pkg, lazy = lazy, examples = examples, …
>  4. pkgdown::build_reference_index(pkg)
>  5. pkgdown::render_page(pkg, "reference-index", data = data_referen…
>  6. pkgdown:::render_page_html(pkg, name = name, data = data, depth =…
>  7. utils::modifyList(data_template(pkg, depth = depth), da…
>  8. base::stopifnot(is.list(x), is.list(val))
>  9. pkgdown:::data_reference_index(pkg)
> 10. meta %>% purrr::imap(data_reference_index_rows, pkg = p…
> 11. base::unlist(., recursive = FALSE)
> 12. purrr::compact(.)
> 13. purrr::discard(.x, function(x) is_empty(.f(x)))
> 14. purrr:::where_if(.x, .p, ...)
> 15. purrr:::map_(.x, .p, ..., .type = "logical", .purrr_error_call …
> 16. purrr:::vctrs_vec_compat(.x, .purrr_user_env)
> 17. purrr::imap(., data_reference_index_rows, pkg = pkg)
> 18. purrr::map2(.x, vec_index(.x), .f, ...)
> 19. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
> 20. purrr:::with_indexed_errors(i = i,

Re: [R-pkg-devel] Suggests with non-CRAN packages

2024-01-03 Thread Duncan Murdoch


On 03/01/2024 11:33 a.m., Josiah Parry wrote:

I have a scenario where I have an exported function that requires the
installation a package that *is not* available on CRAN. The body of the
function is generally:

fx <- function() {
   rlang::check_installed("noncranpkg")
   noncranpkg::gx()
}

As required, this package is in the Suggests field. But this results in a
note:

checking package dependencies ... NOTE
Package suggested but not available for checking: ‘noncranpkg’

Can this be safely ignored?


Uwe said yes, and he's an authority.  But for your users, it might be 
nice to include an Additional_repositories field so they can find the 
package.  This needs to be organized as an actual repository; the drat 
package is a very convenient way to set one up.


Duncan Murdoch

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Re: [R-pkg-devel] Suggests with non-CRAN packages

2024-01-03 Thread Josiah Parry

Lovely, thank you!

On Wed, Jan 3, 2024 at 11:43 AM Uwe Ligges 
wrote:

>
>
> On 03.01.2024 17:33, Josiah Parry wrote:
> > I have a scenario where I have an exported function that requires the
> > installation a package that *is not* available on CRAN. The body of the
> > function is generally:
> >
> > fx <- function() {
> >rlang::check_installed("noncranpkg")
> >noncranpkg::gx()
> > }
> >
> > As required, this package is in the Suggests field. But this results in a
> > note:
> >
> > checking package dependencies ... NOTE
> > Package suggested but not available for checking: ‘noncranpkg’
> >
> > Can this be safely ignored?
>
> Yes.
>
> Best,
> Uwe Ligges
>
>
>
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Suggests with non-CRAN packages

2024-01-03 Thread Uwe Ligges




On 03.01.2024 17:33, Josiah Parry wrote:

I have a scenario where I have an exported function that requires the
installation a package that *is not* available on CRAN. The body of the
function is generally:

fx <- function() {
   rlang::check_installed("noncranpkg")
   noncranpkg::gx()
}

As required, this package is in the Suggests field. But this results in a
note:

checking package dependencies ... NOTE
Package suggested but not available for checking: ‘noncranpkg’

Can this be safely ignored?


Yes.

Best,
Uwe Ligges




[[alternative HTML version deleted]]

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[R-pkg-devel] Suggests with non-CRAN packages

2024-01-03 Thread Josiah Parry

I have a scenario where I have an exported function that requires the
installation a package that *is not* available on CRAN. The body of the
function is generally:

fx <- function() {
  rlang::check_installed("noncranpkg")
  noncranpkg::gx()
}

As required, this package is in the Suggests field. But this results in a
note:

checking package dependencies ... NOTE
Package suggested but not available for checking: ‘noncranpkg’

Can this be safely ignored?

[[alternative HTML version deleted]]

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R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

2024-01-03 Thread Ivan Krylov

On Wed, 3 Jan 2024 13:34:27 +
Daniel Kelley  wrote:

> Error: 
> ! in callr subprocess.
> Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
> ! In index: 1.

Interesting that the actual error messages seem to be completely
empty.

By chance (I was searching for "rlang See `$stdout` for standard
output" because I was curious to know what is this error message
telling the user to subset) I found a bug report that seems relevant
(as it's also about S7, has the same warning and crashes in the same
call to rlang::check_installed):
https://github.com/r-lib/pkgdown/issues/2186

Unfortunately, there's no solution, just two similar-looking cases.

Is there an equivalent of options(error = recover) for callr child
processes? If you can recover the expression evaluated by the child
process, it could be worth executing it directly and walking the call
stack looking at the local variables at the time of the crash.

-- 
Best regards,
Ivan

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[R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

2024-01-03 Thread Daniel Kelley

# Question

Is there an online example online of specializing `plot()` for S7 objects, such 
that `pkgdown::build_site()` will produce webpages?  I ask because I find lots 
of users (of other packages) tend to consult websites made with pkgdown, rather 
than using the online help within R.  I think the problem I am having 
(discussed in the following sections) has to do with my specialization of 
plot().  I say that because when I was using S3 objects in an earlier version 
of my package, `pkgdown::build_site()` worked as intended.

# Background

In my 'mooring' package (https://github.com/dankelley/mooring/tree/S7), I am 
writing code like 
(https://github.com/dankelley/mooring/blob/f70b53ca12e88968f65710c205b50a64f750a99d/R/plot.R#L69)

```R
#' @aliases plot.mooring
#' ETC
`plot.mooring::mooring` <- plot(ETC) ETC
```

to handle objects made with 
(https://github.com/dankelley/mooring/blob/f70b53ca12e88968f65710c205b50a64f750a99d/R/oo.R#L2)

```R
mooringS7 <- S7::new_class("mooring",
package = "mooring",
ETC
```

Built up in Rstudio, with Roxygen2 being used to create documentation, things 
seem to work, e.g.

```R
m <- mooring(anchor(), wire(length = 80), float(), waterDepth = 100)
plot(m)
```

produces a plot as intended, and

```R
?plot.mooring
```

produces documentation as intended.

*However* I encounter a problem comes when I try building a website with

```R
pkgdown::build_site()
```

This yields results as in the next section.  (I apologize for the length. I'm 
including the whole thing because I thought that would be less bothersome than 
writing another email to the list.)

I am not sure how to find the problem, and so I hope that someone on this list 
can point out an example of how to set up `plot()` to work with S7 objects, in 
such a way that documentation can be created with Roxygen2 and websites can be 
made with `pkgdown::build_site()`.

# What pkgdown::build_site() gives

```
> library(pkgdown)
> build_site()
Warning: Failed to parse usage:

S3method(`plot`, ``mooring::mooring``)(
  x,
  which = "shape",
  showInterfaces = TRUE,
  showDepths = FALSE,
  showLabels = TRUE,
  showDetails = FALSE,
  fancy = FALSE,
  title = "",
  mar = c(1.5, 3.5, 3.5, 1),
  mgp = c(2, 0.7, 0),
  xlim = NULL,
  xaxs = "r",
  yaxs = "r",
  type = "l",
  debug = 0,
  ...
)

-- Installing package into temporary library 
== Building pkgdown site ===
Reading from: '/Users/kelley/git/mooring'
Writing to:   '/Users/kelley/git/mooring/docs'
-- Initialising site ---
-- Building home ---
Writing '404.html'
-- Building function reference -
Error: 
! in callr subprocess.
Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
! In index: 1.
ℹ See `$stdout` for standard output.
Type .Last.error to see the more details.
> .Last.error

Error: 
! in callr subprocess.
Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
! In index: 1.
ℹ See `$stdout` for standard output.
---
Backtrace:
1. pkgdown::build_site()
2. pkgdown:::build_site_external(pkg = pkg, examples = examples, run…
3. callr::r(function(..., cli_colors, pkgdown_internet) { …
4. callr:::get_result(output = out, options)
5. callr:::throw(callr_remote_error(remerr, output), parent = fix_…
---
Subprocess backtrace:
 1. pkgdown::build_site(...)
 2. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do…
 3. pkgdown::build_reference(pkg, lazy = lazy, examples = examples, …
 4. pkgdown::build_reference_index(pkg)
 5. pkgdown::render_page(pkg, "reference-index", data = data_referen…
 6. pkgdown:::render_page_html(pkg, name = name, data = data, depth =…
 7. utils::modifyList(data_template(pkg, depth = depth), da…
 8. base::stopifnot(is.list(x), is.list(val))
 9. pkgdown:::data_reference_index(pkg)
10. meta %>% purrr::imap(data_reference_index_rows, pkg = p…
11. base::unlist(., recursive = FALSE)
12. purrr::compact(.)
13. purrr::discard(.x, function(x) is_empty(.f(x)))
14. purrr:::where_if(.x, .p, ...)
15. purrr:::map_(.x, .p, ..., .type = "logical", .purrr_error_call …
16. purrr:::vctrs_vec_compat(.x, .purrr_user_env)
17. purrr::imap(., data_reference_index_rows, pkg = pkg)
18. purrr::map2(.x, vec_index(.x), .f, ...)
19. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
20. purrr:::with_indexed_errors(i = i, names = names, error_call = …
21. base::withCallingHandlers(expr, error = function(cnd) { …
22. purrr:::call_with_cleanup(map2_impl, environment(), .type, .pro…
23. local .f(.x[[i]], .y[[i]], ...)
24. pkgdown:::section_topics(section$contents, pkg$topics, pkg$src_pa…
25. base::rbind(topics, ext_topics(ext_strings))
26. base::rbind(deparse.level, ...)
27. pkgdown:::ext_topics(ext_strings)
28. purrr::map2(pkg, fun, get_rd_from_help)
29. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
30. purrr:::wit

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

Re: [R-pkg-devel] Suggests with non-CRAN packages

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

Re: [R-pkg-devel] Suggests with non-CRAN packages

Re: [R-pkg-devel] Suggests with non-CRAN packages

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

Re: [R-pkg-devel] Suggests with non-CRAN packages

Re: [R-pkg-devel] Suggests with non-CRAN packages

Re: [R-pkg-devel] Suggests with non-CRAN packages

[R-pkg-devel] Suggests with non-CRAN packages

Re: [R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

[R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

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