Hi, On 3/14/25 5:42 AM, Lluís Revilla wrote: > Hi! > > Before moving to git (and shortly after), Bioconductor used to support > these kind of files.
Can you point to where in the documentation these files were supported? > One can still find repositories with these files on code.bioconductor.org. > > As these files are optional and might not even be described by > guidelines they do not bother new developers (or Bioconductor core). > Sure, they can be distracting if someone goes to read the source code > on the repository but so can a README and multiple vignettes. > One needs to familiarize itself with Bioconductor policies and > guidelines to see something as required, encouraged, optional or > forbidden. > > Regarding "It is of interest to minimize the number of files not > relevant to BBS operations." The .Rbuildignore exists so that R > machinery doesn't have to deal with extra files to build and check > packages. Isn't that enough for BBS operations? Our current guidelines were developed as a result of issues with extraneous files and to minimize the amount of bloat in packages. The .Rbuildignore file is not enough as packages sometimes do all sorts of unexpected things that we have to fix. > I heard that Bioconductor is considering using the r-universe > infrastructure to build packages. If it ends up using it I think this > is even a less important concern as these files are allowed there (and > I would say even encouraged). > > But if this is contentious, the CAB could summarize how the community > at large feels about adding those files to the repository. > Or as next month is the joint CAB-TAB joint meeting, it might be a > good moment to talk about this. > > Best, > > Lluís > > PS: .Rprofile is a standard .R file, I'm not sure which relation it > has with a specific IDE. But even IDE's specific files might be a > choice of the maintainers of the package to enable and encourage > community participation within some standards. I meant to write .Rproj > On Tue, 11 Mar 2025 at 17:12, Marcel Ramos Pérez > <marcel.ramospere...@login.cuny.edu> wrote: >> 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://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!UQMRNwXFwFGNEssPVvEgipF409Wcb0z3o6nDuCfLrjCli7p_Y9hqYzFCC-FJ7TfRqMdZ7gmCWdJXBEd9Xx06Osxmr8eXTQ$ >> ____ *Marcel Ramos, MPH* Sr. Data Scientist CUNY Graduate School of Public Health & Health Policy 55 W. 125th Street, 6th Fl.| 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
