[skip vbump] upversion to 0.4.0 #300

donyunardi · 2025-01-22T00:51:40Z

Related to #296

Update NEWS
Update DESCRIPTION and upversion rtables.office and rtables to released version

github-actions · 2025-01-22T00:56:51Z

Unit Tests Summary

1 files 19 suites 28s ⏱️
197 tests 197 ✅ 0 💤 0 ❌
337 runs 337 ✅ 0 💤 0 ❌

Results for commit 371f13f.

♻️ This comment has been updated with latest results.

donyunardi · 2025-01-22T18:40:19Z

I removed Remotes entry for rtables.officer because the package is now available in CRAN.

donyunardi · 2025-01-22T19:10:22Z

Got a NOTE when checking against R-oldrelease:
https://win-builder.r-project.org/9P7T8DL5kaJ3/00check.log

* checking examples ... [54s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
          user system elapsed
Reporter 19.77   0.19   19.97
Renderer 15.83   0.68   17.48

But no NOTES in R-release and R-devel:
https://win-builder.r-project.org/o5xCZFZZW4ug/00check.log
https://win-builder.r-project.org/uV31AS5CA6hW/00check.log

I think we're good to go.

donyunardi · 2025-01-23T00:26:32Z

Submitted to CRAN. Awaiting Feedback.

donyunardi · 2025-01-23T00:40:32Z

Got automated feedback not passing under Debian:
https://win-builder.r-project.org/incoming_pretest/teal.reporter_0.4.0_20250123_012612/Debian/00check.log

Dear maintainer,

package teal.reporter_0.4.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests (additional issue checks):
Windows: <https://win-builder.r-project.org/incoming_pretest/teal.reporter_0.4.0_20250123_012612/Windows/00check.log>
Status: OK
Debian: <https://win-builder.r-project.org/incoming_pretest/teal.reporter_0.4.0_20250123_012612/Debian/00check.log>
Status: 1 NOTE

Last released version's CRAN status: OK: 13
See: <https://cran.r-project.org/web/checks/check_results_teal.reporter.html>

CRAN Web: <https://cran.r-project.org/package=teal.reporter>

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

More details are given in the directory:
<https://win-builder.r-project.org/incoming_pretest/teal.reporter_0.4.0_20250123_012612/>
The files will be removed after roughly 7 days.

*** Strong rev. depends ***: teal teal.modules.clinical teal.modules.general

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-windows-x86_64
Check: *, Result: OK


Flavor: r-devel-linux-x86_64-debian-gcc
Check: examples, Result: NOTE
  Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
  Reporter 6.788  0.032   6.820
  Renderer 5.886  0.172   6.097

donyunardi · 2025-01-23T01:26:30Z

I see iris is being used on the test cases of Renderer and Reporter. One way that I could think of is to make a smaller subset of iris or use other dataset that are smaller like cars.

@insightsengineering/nest-core-dev what do you think?

llrs-roche · 2025-01-23T08:33:14Z

I found this same problem on #299 , I explored it a bit and I think it is a problem with roxygen @examplesIf, see also #248. I don't think changing datasets will reduce computing time. We might be able to reduce (more)time if instead of having each method create a new card and reporter we reused one. It might be harder to follow individual methods examples but it will probably make the examples faster.

…renderer

donyunardi · 2025-01-23T23:47:48Z

It turns out, we have the same message in our r-hub action as well in the main branch (Debian == gcc12):
https://github.com/insightsengineering/teal.reporter/actions/runs/12850103218/job/35829405265#step:8:119

After investigation, I decided to just remove the second append_table() method for iris dataset.

The pipeline is now completed without NOTE:
https://github.com/insightsengineering/teal.reporter/actions/runs/12940202534/job/36093952669#step:8:118

What I did was:

Removed duplicated getNamespace from examples
Removed append_table(iris) since we already another append_table() in the example

pawelru · 2025-01-24T09:29:03Z

It would be the best to use profiler tools to identify performance bottlenecks. I think that you are guessing here.

pkgload::run_example("./man/Reporter.Rd") |> profvis::profvis()

Currently the main performance bottleneck is converting rtables to flextable (which is btw happening outside of this package). Hance I would rather remove / shorten rtables related example.

pawelru · 2025-01-24T09:34:56Z

Sorry I was too fast and made mistake

rtables to flextable is responsible for this:

Whereas data.frame to flextable is responsible for this:

In this case - reducing examples with data.frames would actually help. I don't know if the size matter though...

BTW: why do force conversion of data.frame to flextable? It looks like an expensive operation.

vedhav · 2025-01-24T10:00:34Z

why do force conversion of data.frame to flextable? It looks like an expensive operation.

I'd have to check, but it could be because of the output render formats. flextable renders in all the formats easily, I'm not sure about rtables.

gogonzo · 2025-01-24T10:33:04Z

BTW: why do force conversion of data.frame to flextable? It looks like an expensive operation.

data.frame needs to be converted to display it in the document. There are several design pitfalls, the most serious:

too early conversion during *Block initialization (via $set_content). It should rather be converted when object is rendered (in Renderer or previewer). Package needs refactor and some discussions took place in a hotel lobby during useR! last year ;] (with @chlebowa @averissimo )

I'd have to check, but it could be because of the output render formats. flextable renders in all the formats easily, I'm not sure about rtables.

flextable is used to "easily" convert object to Rmd and HTML (see Renderer$renderRmd, block_to_html())

pawelru · 2025-01-24T11:00:20Z

too early conversion during *Block initialization (via $set_content). It should rather be converted when object is rendered (in Renderer or previewer).

Yeah that's exactly it. Probably not worth to postpone the release because of that but I think it's important.

Also posting this just to show you how to handle "examples takes too long" type of problems.

gogonzo · 2025-01-24T11:06:00Z

Yeah that's exactly it. Probably not worth to postpone the release because of that but I think it's important.

It is not justv about TableBlock. Plots for example are saved into file during PictureBlock initialization. I'm not a fan to do these changes now as we already know that the whole package needs to be revisited.

donyunardi · 2025-01-24T17:52:08Z

Thanks @pawelru! Your advise will come in handy moving forward if we run into this type of issue again when submitting to CRAN.

Also, as you mentioned, refactoring the examples is not worth to postpone the release, especially we're thinking about refactoring teal.reporter with this issue

I will move forward with the release.

donyunardi · 2025-01-24T18:45:35Z

Submitted. Awaiting CRAN feedback.

donyunardi · 2025-01-24T19:34:03Z

made it to CRAN

[skip vbump] upversion to 0.4.0

956f054

donyunardi added the core label Jan 22, 2025

m7pr approved these changes Jan 22, 2025

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m7pr self-assigned this Jan 22, 2025

donyunardi added 2 commits January 22, 2025 10:36

Merge branch 'main' into release-candidate-v0.4.0

93bcbe7

remove Remotes entry for rtables.officer

b1c54da

donyunardi linked an issue Jan 23, 2025 that may be closed by this pull request

[CRAN Release]: 0.4.0 #296

Closed

32 tasks

donyunardi added 2 commits January 23, 2025 12:45

optimize Renderer example

6ef8994

remove the second append_table for iris in examples for reporter and …

371f13f

…renderer

donyunardi requested a review from m7pr January 23, 2025 23:47

m7pr approved these changes Jan 24, 2025

View reviewed changes

donyunardi merged commit 4930f11 into main Jan 24, 2025
62 checks passed

donyunardi deleted the release-candidate-v0.4.0 branch January 24, 2025 19:34

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[skip vbump] upversion to 0.4.0 #300

[skip vbump] upversion to 0.4.0 #300

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[skip vbump] upversion to 0.4.0 #300

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