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@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. > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
