Re: [R-pkg-devel] Missing ggPMX causing failure for nlmixr2rpt

[Lluís Revilla]

Dear John,

I think the problem is that the package ggPMX is suggested, but
nlmixr2rpt isn't prepared for when it isn't available.
In such cases, a package shouldn't fail the checks.

>From the CRAN policies https://cran.r-project.org/web/packages/policies.html :
"A package listed in ‘Suggests’ or ‘Enhances’ should be used
conditionally in examples or tests if it cannot straightforwardly be
installed on the major R platforms. (‘Writing R Extensions’ recommends
that they are always used conditionally.)"

Among other things in the file test-rptnlmixr.R you load several
suggested packages without checking if they are available.
You should only run those tests and examples that need those packages
if they are available.
Checking via:  if (requireNamespace("ggPMX", verbose = FALSE) could be enough

There's also an example that seems to be failing, I didn't understand
the reason behind it but it might be related.

Best,

Lluís


On Fri, 2 Jun 2023 at 02:49, John Harrold  wrote:
>
> Hello,
>
> I recently got a "Dear Maintainer" email from Brian Ripley. It was
> concerning the nlmixr2rpt package I maintain:
>
> https://cran.r-project.org/web/checks/check_results_nlmixr2rpt.html
>
> It looks like there is an error on r-release-linux-x86_64 that is causing
> it. If I'm reading that correctly there is a problem finding ggPMX on that
> flavor. If I look at the check results for ggPMX it seems to be building
> fine there:
>
> https://cran.r-project.org/web/checks/check_results_ggPMX.html
>
> Am I reading that correctly that ggPMX not being found is the cause of my
> issues? If that's the case and it seems to be present now, can I just wait
> and let CRAN machines find it? Or should I just resubmit with those pieces
> removed from the version I submit to CRAN?
>
> --
> Thank you,
> John
> :wq
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] Missing ggPMX causing failure for nlmixr2rpt

[Ivan Krylov]

On Thu, 1 Jun 2023 17:48:49 -0700
John Harrold  wrote:

> Am I reading that correctly that ggPMX not being found is the cause
> of my issues?

Your package got flagged by the additional test, "noSuggests", where
only the packages you have a hard dependency upon are available:
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/README.txt

By default, install.packages() does not install the packages listed in
Suggests:, so it's important for your package to work even if all
packages listed there are not available. See WRE 1.1.3.1

for information on how to add checks into your documentation examples /
tests / vignettes.

If ggPMX is vitally important for your package to work, move it to
Imports:, and you won't have to alter all your tests.

-- 
Best regards,
Ivan

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