Anatoly, delaying dependency on R 4.4 until October would mean 6 months of Bioconductor release requiring an old release of R for users. Bioconductor developers developing against r-devel means that users get a new Bioconductor release that works immediately on the new R. And I think a main purpose of a 6 month devel and release cycle is to provide a comfortable period for everyone to work out new features and bugs and to resolve downstream consequences that may arise. Delaying the Bioconductor release by a week or something might actually encourage a habit of last-week bug fixes that should be discouraged 😉. I really can’t see any way around requiring developers to test against r-devel without sacrificing timeliness and reliability for users. There are also Docker and GitHub Actions options that don’t require installing r-devel to test against it.
I think many HPC clusters now support Singularity, which is a more reliable and easier way to run packages with a compatible version of R. Installing from GitHub on an old version of R has no guarantees of being tested or working correctly even if it installs without error, and I see as a sacrifice of software reliability for convenience that can be avoided with Singularity or regular R updates. Henrik, if Bioconductor releases weren’t tied to R releases, how could Bioconductor test them? I guess like CRAN where as long as a package says it depends on R >= 2.0 then you’re free to try installing on 2.0 even though the combination has never been tested? Maybe I worry too much about such testing since CRAN seems OK anyways, as far as we know? ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Anatoly Sorokin <lpto...@gmail.com> Sent: Thursday, April 4, 2024 10:28:47 PM To: Kern, Lori <lori.sheph...@roswellpark.org> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Important Bioconductor Release Deadlines Hi all, I'm sorry for the complaint, but do you really think it is wise to make the new release dependent on the R version which has not released yet? I have a lot of R-related projects going on apart from maintaining the Bioconductor package and I'm not comfortable installing the unreleased version of R on my machine and spending time debugging it in the case of possible problems. At the same time, I have an error, possibly caused by a new version of GO.db package, which BioNAR is dependent upon and I can not fix it until the R 4.4 release on the 24th of April when I would have less than a day to fix the possible problem and fit into R CMD build and R CMD check by the Friday April 26th. Don't you think this is a rather tight time frame? Sorry once again, for the complaint. Cheers, Anatoly On Tue, Mar 26, 2024 at 11:06 PM Kern, Lori via Bioc-devel < bioc-devel@r-project.org> wrote: > Import update: The Bioconductor Release will be May 1 following the > release of R 4.4 on April 24. > > The Bioconductor 3.18 branch will be frozen Monday April 15th. After that > date, no changes will be permitted ever on that branch. > > The deadline for devel Bioconductor 3.19 for packages to pass R CMD build > and R CMD check is Friday April 26th. While you will still be able to make > commits past this date, This ensures any changes pushed to > git.bioconductor.org are reflected in at least one build report before > the devel branch will be copied to a release 3.19 branch. > > Cheers, > > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > 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 > [[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
