R CMD check sometimes wants dependency on specific R versions, for example when the file format changed (forgot which version .. was it 3.6). But that warning is emitted when it tests the package utilizes version-specific stuff.
I get that Bioc doesn't check under older versions. That is intentional. But that is different from the check asking for a specific version for no particular reason (as far as I can ascertain). Best, Kasper On Thu, Apr 8, 2021 at 8:13 PM Henrik Bengtsson <henrik.bengts...@gmail.com> wrote: > > 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 > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
