[Bioc-devel] BiocCheck and version requirement

[Henrik Bengtsson]

> 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.Shepherd using 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 <kasperdanielhansen using gmail.com>
> Sent: Thursday, April 8, 2021 1:33 PM
> To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
> Cc: bioc-devel <bioc-devel using 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.Shepherd using roswellpark.org<mailto:Lori.Shepherd using 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-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Kasper Daniel Hansen <kasperdanielhansen using gmail.com<mailto:kasperdanielhansen using gmail.com>>
> Sent: Thursday, April 8, 2021 9:44 AM
> To: bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using 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
>
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> --
> Best,
> Kasper
>
>
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