Hi Leonardo, BioC doesn't oppose an Rmd -- you just need to include the eval=F in the package installation code chunk. If helpful, please have a look at our package GitHub: https://bioconductor.org/packages/release/bioc/html/rhinotypeR.html
Best, Martha On Tue, 11 Mar 2025 at 14:05, Leonardo Collado Torres <lcollado...@gmail.com> wrote: > Hi, > > What's the issue with having a README.md and a README.Rmd file on the > Git repo for a Bioconductor package? > > There's no such mention at > https://contributions.bioconductor.org/readme.html?q=readme#readme. > Also, a README.Rmd file can be included on the .Rbuildignore file > without any issues. > > It feels weird to just include the README.md and not the README.Rmd. > That is, just including the rendered version makes it hard to update > later. > > On the flip side, just including the README.Rmd version means that you > can't include the rendered version. > > See other points in favor of both versions at > https://r-pkgs.org/other-markdown.html#readme.rmd-and-readme.md. > > Is it a matter of automating a test in BiocCheck to make sure that > README.Rmd files are included in .Rbuildignore files? In case you are > concerned about R code being executed on your machines from those > README.Rmd files. Or auto-checking that any images used in the > README.md files are part of the .Rbuildignore files? > > > Anyways, I have known for a few years [1] that I think very > differently as I'm in favor of including files on Git repos that help > users & new developers and that can be excluded from packages source > tarballs thanks to .Rbuildignore. I overall feel that Bioc's push for > more strict control of which files are allowed is detrimental to both > users as well as new developers. Other examples are: > > * the biocthis dev/ folder created by > > https://lcolladotor.github.io/biocthis/reference/use_bioc_pkg_templates.html > : > in particular the dev/04_update.R script is one that includes commands > new package developers typically forget to run after an update to > source files, like devtools::document() devtools::build_readme(). > * the *.Rproj file which helps ensure some options are common across > the package author team (not all packages are made by 1 person!). This > one is listed at > > https://contributions.bioconductor.org/general.html?q=unnec#undesirable-files > without much explanation. > * pkgdown and codecov yaml config files > > If the above were just NOTEs on BiocCheck that are encouraged, but not > enforced during review, that would be one thing. Actually, from > searching https://github.com/Bioconductor/BiocCheck I don't see > anything about pkgdown or codecov yaml files, nor anything about > README.md and README.Rmd. I do see .Rproj mentioned at > > https://github.com/Bioconductor/BiocCheck/blob/3e6bc8d50cbb34a8f1eeb13611ffefceed7461b0/R/BiocCheckGitClone.R#L2 > which sadly does lead to en ERROR as noted at > > https://www.bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#bad-file-check > instead of a NOTE (I'd actually vote for fully allowing them, but a > NOTE would be ok to compromise on). > > Best, > Leo > > [1] https://github.com/lcolladotor/biocthis/issues/21 > > Leonardo Collado Torres, Ph. D. > Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT > Assistant Professor, Department of Biostatistics > Johns Hopkins Bloomberg School of Public Health > 855 N. Wolfe St., Room 382 > Baltimore, MD 21205 > lcolladotor.github.io > lcollado...@gmail.com > > _______________________________________________ > 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
