Re: [R-pkg-devel] [Rd] static html vignette

[Jan Gorecki]

I may add two cents on that as we recently made this change in data.table.
Using markdown package instead of rmarkdown as a vignette engine reduced
burden caused by extra dependencies tremendously. Moreover it made package
to not even need c++ compiler, as knitr and markdown both (and their
recursive deps) are pure C with no C++.
Gains were huge. Deps installation time from 12min to 30sec. CI pipeline
compute minutes saving around 100min on a single workflow.

But there is even a better news (so be sure to upvote), that knitr may not
be required to render Rmd at all in near future. For details see
https://github.com/rstudio/markdown/issues/109


On Thu, Jan 4, 2024, 22:27 Adrian Dușa  wrote:

> On Thu, Jan 4, 2024 at 10:44 PM Uwe Ligges <
> lig...@statistik.tu-dortmund.de>
> wrote:
>
> > On 04.01.2024 21:23, Duncan Murdoch wrote:[...]
> > > Users aren't forced to install "Suggests" packages.  That's a choice
> > > they make.  The default for `install.packages()` is `dependencies =
> NA`,
> > > which says to install hard dependencies (Imports, Depends, LinkingTo).
> > > Users have to choose a non-default setting to include Suggests.
> >
> > Also note that the maintainer builds the vignette whe calling
> > R CMD build
> > CRAN checks whether the vignette can be build.
> > If a user installs a package, the already produced vignette (on the
> > maintainers machine by R CMD build) is instaled. There is no need for
> > the user to install any extra package for being able to look at the
> > vignettes.
> >
>
> I see... then I must have tested with dependencies = TRUE thinking this
> refers to hard dependencies (one more reason to read the documentation
> properly).
>
> Thank you,
> Adrian
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] CRAN submission struggle

[Ivan Krylov]

On Sat, 6 Jan 2024 15:16:01 +0300
Ivan Krylov  wrote:

> Congratulations! I also get the single expected NOTE in my checks.

Apologies for the double e-mail, but I've read the code now, and
wrapping the example of your only function in \dontrun{} will most
likely not be allowed.

Is it really the case that you cannot remove a single row from the
example dataset without making the example crash? It may help to write
a function that would remove rows one by one, make sure that the
example still runs, and keep doing that until not a single row can be
removed. The complexity is terrible (something like O(n^k)), but let it
run for a while, and maybe it'll reduce the dataset enough to fit in
the example time limit.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] CRAN submission struggle

[Ivan Krylov]

On Sat, 6 Jan 2024 13:50:49 +0200
Christiaan Pieterse  wrote:

> Is there a way to confirm that this package is ready for submission?
> I submitted it to https://win-builder.r-project.org/ and
> https://mac.r-project.org/macbuilder/submit.html and
> https://builder.r-hub.io/. All of these seem to only show the
> expected new submission note.

Congratulations! I also get the single expected NOTE in my checks.

This may be your last chance to rename the package from iopspackage to,
say, "IOPS". If you go over the package and the CRAN policy at
 one last time
and deem the package compliant, it should be ready for submission.

The CRAN reviewer may find additional problems and ask you to fix them,
but you are likely most of the way there.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] CRAN submission struggle

[Christiaan Pieterse]

Good day

I think I finally have a final package that only yields the expected 'New
submission' note.
The package is available at:
https://github.com/WoutersResearchGroup/R-IO-PS/tree/CRAN-prep.

Is there a way to confirm that this package is ready for submission?
I submitted it to https://win-builder.r-project.org/ and
https://mac.r-project.org/macbuilder/submit.html and
https://builder.r-hub.io/. All of these seem to only show the expected new
submission note.

I see the CRAN package submission web form is unavailable until the 8th, so
any confirmation that my package should be fine for submission would be
appreciated.

Thank you
Christiaan

On Tue, 2 Jan 2024 at 14:59, Uwe Ligges 
wrote:

>
>
> On 29.12.2023 09:13, Greg Hunt wrote:
> > Christaan,
> > The elapsed time note is because CRAN expects that examples will be
> > configured to run single threaded and some package that you use, or a
> > package used by a package that you use is multi-threading by default and
> > using more CPU time than clock time. If you cannot figure out how to
> > reconfigure the multi-threaded package, a number of people have found
> that
> > the simplest thing to do is disable running the example (which reduces
> the
> > effective test coverage provided by the example).
>
>
> No and no:
>
> 1.
>user system elapsed
> IOPS 10.06   3.35   35.04
>
> suggests that either the machines this ran on is heavily loaded (so that
> elapsed >> user) or something is waiting like some internet access. [For
> multithreading it would be user > elapsed.]
>
> 2. The solution is not to exclude examples ebtirely, as we need runtime
> checks.
>
> For internet access: Set a timeout and let the exampe fail gracefully in
> case web access takes more than, e.g., 2. sec.
>
> In general: Please reduce each example to less than 5 sec.
>
> So use small toy examples. If you really want to add rel world examples
> that may take longer, then add them in addition to toy examples and wrap
> in \donttest{}.
>
> Best,
> Uwe Ligges
>
>
>
>
>
>
>
>
> >
> > I haven’t encountered the miktex exception file before but i suspect its
> a
> > side effect of a miktex error. Packages should not leave files behind in
> > the temp directory. If you expect a miktex error you need to remove the
> > file. If you don’t you need to track down and fix or work around the bug.
> > The build process is really a quality check on your package.
> >
> > Greg
> >
> > On Fri, 29 Dec 2023 at 3:01 am, Christiaan Pieterse <
> > pietie.cjp.1...@gmail.com> wrote:
> >
> >> Hi,
> >>
> >> Thank you for showing the difference in the ExampleTradeData. I've fixed
> >> this by adding a .Gitignore file and a "data-raw" folder to load the
> >> ExampleTradeData. I hope I did this correctly. When I check the package
> (
> >> https://github.com/WoutersResearchGroup/R-IO-PS/tree/CRAN-prep) in
> >> RStudio.
> >> I only get 3 notes (see below), and if I run it in PositCloud, it
> crashes
> >> or yields the same 1 ERROR and 2 NOTES result as before. Why might this
> be?
> >> Is it a problem or is it fine if I continue working in RStudio since I
> >> cannot increase the specs in PositCloud because I'm working on a
> research
> >> group account?
> >>
> >> Here are the 3 notes I receive in RStudio:
> >>
> >> The first is the expected New Submission Note.
> >>
> >> The second is the runtime that is too long:
> >> * checking examples ... [43s] NOTE
> >> Examples with CPU (user + system) or elapsed time > 5s
> >>user system elapsed
> >> IOPS 10.06   3.35   35.04
> >> How can I reduce this time? I'm not sure how to reduce the size of my
> >> ExampleTradeData without the check giving errors when running the
> example.
> >>
> >> The third note I am unsure what it means:
> >> * checking for detritus in the temp directory ... NOTE
> >> Found the following files/directories:
> >>'lastMiKTeXException'
> >>
> >> Kind regards
> >> Christiaan
> >>
> >> On Thu, 28 Dec 2023 at 15:55, Ivan Krylov 
> wrote:
> >>
> >>> Hi Christiaan,
> >>>
> >>> В Thu, 28 Dec 2023 14:57:55 +0200
> >>> Christiaan Pieterse  пишет:
> >>>
>  Still, I couldn't figure out why I ran into this problem, so I
>  created a test file called "Test Example.R" (available at the same
>  GitHub repository:
>  https://github.com/WoutersResearchGroup/R-IO-PS/tree/CRAN-prep).
> >>>
> >>> I see you're always adding or updating files to the GitHub repo by
> >>> means of uploading. While that's certainly one way to use GitHub, it's
> >>> combines the least convenient aspects of two approaches to using
> GitHub.
> >>>
> >>> With GitHub purely in the browser, GitHub is just a website where you
> >>> keep and edit code, running nothing else on the local computer. Code
> >>> can be run in Codespaces or using GitHub Actions. Microsoft will want
> >>> to be paid money to run code on their computers.
> >>>
> >>> With GitHub as a Git remote, there is a local checkout [*] that's kept
> >>> in sync with GitHub by means of commits [**] and pushe