Thanks Lori for the clarification. If the purpose of the check is to capture the R version upon submission to Bioconductor, then it makes sense. I would suggest a bit of clarification in the docs though. Also, a warning is not produced when "Depends: R (xxx)" is completely missing in DESCRIPTION. If my understanding is correct, a warning should also be given in that case.
For my package, I plan to keep every thing as is in a pre-release version (0.98.0), and then pump R version upon submission to tracker (v0.99.0), skipping CI tests for bioc-release. Hope this will be acceptable. Cheers. Ahmed. On Wed, 27 Mar 2019 at 21:23, Shepherd, Lori <lori.sheph...@roswellpark.org> wrote: > Bioconductor has release cycles to ensure that packages are building > cleaning and working with dependency at any given time. The version would > not have to be updated each release, it is an indication of the version of > R used at the time of submission and to give a base line of what versions > were minimally working. > > > Bioconductor builds packages nightly on release and devel branches. we > assume any development will be pushed to the devel branch to ensure if a > package functionality changes and packages that depend on it may break that > there is some indication of that to give package maintainers an environment > to update and adapt, and that there is still the release stable environment > of working dependencies. > > > If your package is already in Bioconductor it is safe to ignore this > warning when running the testing environment (or if you feel like disabling > it you could use the BiocCheck option --no-check-R-ver) However, if > your package is in the submission tracker we will generally insist on > updating this R version dependency for the reasons stated. For example, > there have been many significant changes to R from 3.5 to 3.6 that effected > a lot of packages and required some major changes, we would have no way to > test or guarantee that a package can work on a previous version and be able > to grab all the correct versions of packages for a past point in time > (beside current release/devel). If you really feel strongly about this you > could still submit your package and argue your case to the reviewer - we > sometimes make an exception but it is not the norm. > > > Hope this helps with clarification > > Cheers, > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Ahmed > Mohamed <moha...@kuicr.kyoto-u.ac.jp> > *Sent:* Wednesday, March 27, 2019 12:54:14 AM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] Bioc_check on devel - Checking R Version > dependency warning > > Hi all, > > I noticed that bioc_check on devel checks for R version dependency, and > produces a warning to change R dependency to 3.6 (currently set as R >= > 3.5.0). Just quickly looking at Bioconductor packages, it seems that at > least half of the packages will have this warning, if tested. It also means > that packages will need to change R dependency each release cycle (and > different R versions for release and devel). > > To be honest, I am not fully convinced also on the rationale behind it. > Quoting > > http://master.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#version-checks > > "BiocCheck checks to make sure that the R version specified matches the > version currently used by *Bioconductor*. This prevents the package from > being used in earlier versions of R, which is not recommended and is a > frequent cause of user confusion (WARNING)." > > Currently, I am using TravisCI to Bioc_check my package on both release and > devel modes, so it is not also possible to change the R version as > suggested in the warning. I wonder if there is a possible work around, > other than looking the other way. > > Link to build here: > https://travis-ci.org/ahmohamed/lipidr/jobs/511789232#L5673 > > Cheers. > Ahmed. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
