[Bioc-devel] BiocCheck and version requirement

[Kasper Daniel Hansen]

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.bengtsson using 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.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
> >
> >         [[alternative HTML version deleted]]
> >
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> > --
> > Best,
> > Kasper
> >
> >
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-- 
Best,
Kasper

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