Hi Leo! As Martha responded, there is no issue with having a README.Rmd in the package folder. (The section is not so clear and could use some revision) Note that some authors maintain a README.md file without an Rmd. For some of my packages, I re-use the vignette to generate the README.md file.
But the bigger question is here "how much of the development environment do we want to allow in the package files?" It is not so clear where to draw this line. IMO, having all the supporting developer files may help for didactic purposes but for the purposes of package functionality, they have little bearing. If one starts to add all sorts of files, they would be distracting and possibly overwhelming to new developers. As may often happen, developers (myself included) forget to remove old files from their packages allowing the cruft to accumulate. It is of interest to minimize the number of files not relevant to BBS operations. I agree, an error for the .Rprofile file is a bit too strict and could be flagged with a NOTE. Though this may not be so relevant for Positron users :) Best regards, Marcel On 3/11/25 10:00 AM, Leonardo Collado Torres wrote: > * This email originates from a sender outside of CUNY. Verify the sender > before replying or clicking on links and attachments. * > > 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://urldefense.com/v3/__https://contributions.bioconductor.org/readme.html?q=readme*readme__;Iw!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-ofA_t2Zo$ > . > 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://urldefense.com/v3/__https://r-pkgs.org/other-markdown.html*readme.rmd-and-readme.md__;Iw!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-oT1xpgL8$ > . > > 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://urldefense.com/v3/__https://lcolladotor.github.io/biocthis/reference/use_bioc_pkg_templates.html__;!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-oA2u6Uo4$ > : > 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, likedevtools::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://urldefense.com/v3/__https://contributions.bioconductor.org/general.html?q=unnec*undesirable-files__;Iw!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-oQbLf9-k$ > 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 > searchinghttps://urldefense.com/v3/__https://github.com/Bioconductor/BiocCheck__;!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-ozcncjiQ$ > 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://urldefense.com/v3/__https://github.com/Bioconductor/BiocCheck/blob/3e6bc8d50cbb34a8f1eeb13611ffefceed7461b0/R/BiocCheckGitClone.R*L2__;Iw!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-ovxrWpLs$ > which sadly does lead to en ERROR as noted at > https://urldefense.com/v3/__https://www.bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html*bad-file-check__;Iw!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-oG3n79eQ$ > 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://urldefense.com/v3/__https://github.com/lcolladotor/biocthis/issues/21__;!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-oWuxf7xw$ > > 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://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!Q_N-tSpOLq_jYv9eiaqg8ADaED9WXdcKZptW6ptp0VaLJaEj_h06XkG_zkGmu6GCqCSgEVAiwLDeMa1XMV-ohkEMrY0$ -- ____ *Marcel Ramos, MPH* Sr. Data Scientist CUNY Graduate School of Public Health & Health Policy 55 W. 125th Street, Room 621| New York, NY 10027 marcel.ra...@sph.cuny.edu <mailto:marcel.ra...@sph.cuny.edu> | (646) 364-9585 sph.cuny.edu <https://sph.cuny.edu> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
