[Bioc-devel] 3 unit tests skipped for CytoPipeline package on Bioc devel

[Philippe Hauchamps]

Hi Martin,

Thanks a lot for your thorough answer, this is now crystal clear 😊
And indeed, deactivating vdiffr::expect_doppelganger() as a default – outside local and GHA unit testing – is a good idea, as these tests regularly issue false positives.

Have a nice day,

Philippe

De : Martin Morgan <mtmorgan.xyz using gmail.com>
Envoyé : 19 October 2024 19:37
À : Philippe Hauchamps <philippe.hauchamps using uclouvain.be>
Cc : bioc-devel using r-project.org
Objet : Re: [Bioc-devel] 3 unit tests skipped for CytoPipeline package on Bioc devel

Vous n’obtenez pas souvent d’e-mail à partir de mtmorgan.xyz using gmail.com<mailto:mtmorgan.xyz using gmail.com>. Pourquoi c’est important<https://aka.ms/LearnAboutSenderIdentification>
I looked at the first reported skip test-gating.R:42:5 and see https://code.bioconductor.org/browse/CytoPipeline/blob/devel/tests/testthat/test-gating.R#L42. I googled for the help page of `vdiffr::expect_doppelganger` https://vdiffr.r-lib.org/reference/expect_doppelganger.html and saw the `can` argument — the documentation indicates that the test is disabled on ‘CRAN’, but actually testthat relies on an environment variable ’NOT_CRAN’ to be defined for the test to run https://testthat.r-lib.org/reference/skip.html . `devtools::test()` defines this variable, but R CMD check (and hence the Biocondcutor build system) does not, so the test is skipped.

Once the test is skipped on line 42, then all the remaining lines of that `testthat()` expression, including several other calls to `expect_doppelganger()`, are also skipped but silently (the code is never evaluated).

You could add `cran = TRUE` as an argument if you disagree with the arguments on `?expect_doppelganger()` as to why this might be a bad idea.

Martin


On Oct 17, 2024, at 8:57 AM, Philippe Hauchamps via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>> wrote:

Hi dear members of Bioc-devel community,

Recently I noticed a 'strange' log in the BUILD/CHECK reports of CytoPipeline, one of the package I am currently maintaining, on Bioc-devel:
https://bioconductor.org/checkResults/devel/bioc-LATEST/CytoPipeline/teran2-checksrc.html

   Skipped tests (3)
• On CRAN (3): 'test-gating.R:42:5', 'test-ggplots.R:185:5',
 'test-ggplots.R:310:5'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 248 ]

It seems three of my unit tests (using testthat) are skipped, while I can't remember having deactivated any of my tests using testthat.

These 3 tests have something in common, they all use the vdiffr package. However, many other unit tests do also use vdiffr (vdiffr::expect_doppelganger()).

Would you have an clue about what might be happening ?

Thanks a lot,

Best wishes,

Philippe Hauchamps.


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