> I believe in the past we tried suggesting removing a R dependency altogether > but that R CMD check complained not having an R dependency? Maybe someone > remembers more about this.
There are no such requirements in 'R CMD check'. The only requirement around 'Depends: R (>= x.y.z)', if specified, is with 'R CMD check --as-cran' that requires z == 0. In other words, you can submit a package to CRAN that depends on a specific patch version, e.g. either R (>= 4.0.0) or R (>= 4.1.0) but not say R (>= 4.0.2) resulting in: * checking DESCRIPTION meta-information ... WARNING Dependence on R version ‘4.0.2’ not with patchlevel 0 In the bigger picture: I argue that Bioconductor's dependency on R version is a major, unnecessary(*) disadvantage and adds barriers between the Bioconductor community and the rest of the R community resulting in many lost opportunities and cross-pollination. (*) I know the arguments, but I think there are better solutions already available that do not enforce specific R versions on users and thereby limit them, e.g. when they want to a single Bioconductor package with zero dependencies in their workflow. As a way forward, I'd suggest that Bioconductor makes it a long-term target to make it possible for any R user to install Bioc packages with a regular install.packages() call - I think that can be achieved. /Henrik On Thu, Apr 8, 2021 at 10:39 AM Kern, Lori <lori.sheph...@roswellpark.org> wrote: > > From a Bioconductor R perspective, we can't tell if the package would work > with a lesser version of R or lower versions of any package dependencies. We > accept packages and have requirements to ensure packages can run. > You can always have another github branch.... > > I believe in the past we tried suggesting removing a R dependency altogether > but that R CMD check complained not having an R dependency? Maybe someone > remembers more about this. > > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Kasper Daniel Hansen <kasperdanielhan...@gmail.com> > Sent: Thursday, April 8, 2021 1:33 PM > To: Kern, Lori <lori.sheph...@roswellpark.org> > Cc: bioc-devel <bioc-devel@r-project.org> > Subject: Re: [Bioc-devel] BiocCheck and version requirement > > But why is it even a warning? The submission policy is that warnings are > discouraged. This means that developers will adapt to this warning. > > The check is also against the policies on the website which state you don't > need a formal dependency. > > Best, > Kasper > > On Thu, Apr 8, 2021 at 3:53 PM Kern, Lori > <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> wrote: > This requirement has been around for awhile. New package submissions are > checked against the devel version of Bioconductor. At the moment this is R > devel (R 4.1) and Bioconductor packages in devel for 3.13. Given that > Bioconductor releases are closely tied to a R release, and changes in R can > (and have) had great consequences for package functionality, we can not > guarantee a package will work on any previous version of R or with previous > versions of packages. > It is why it is a warning and not an error > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Bioc-devel > <bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> > on behalf of Kasper Daniel Hansen > <kasperdanielhan...@gmail.com<mailto:kasperdanielhan...@gmail.com>> > Sent: Thursday, April 8, 2021 9:44 AM > To: bioc-devel <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> > Subject: [Bioc-devel] BiocCheck and version requirement > > The latest BiocCheck (well, it may have been around for a bit) _requires_ > the package to have a R >= 4.1 dependency. > > That seems new to me. Right now it's a bit irritating, because if you're > submitting a package that works with latest stable release, you are now > prohibited from installing it from Github into your stable Bioc version. > > Traditionally, we have not enforced this I think, even though we all know > of the implicit dependency. > > -- > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list > https://secure-web.cisco.com/1Zqtuoo0O2aKBea_yHofM_QCv72B3JNIupD47xAVitntUD9FgXVvT4yX66u57RWFhMonvou61R_vk6u1LgIM5J8qpHXw4gXWyAxGlZFJEH--5tT-UESMe6_L4bbB6jIcOfYl0J5FI0gucNH0boaxPdv4-It-V5j3TPd2bd5Er3K7MHNVFhqgA5bs84nYYGnvBuOVns86_d2q_mkKzVTHay7GQUxlJhDGVxQbxlwyKvaVPNraVZJKI3lQzwTpavNpm7CpFuIOaDv9a9-euSOlKn3NYMdkPxNfAHv3u2sI1vZ_1ww4KU4c5TgGsp-ard5Ix/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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. > > > -- > Best, > Kasper > > > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
