[Bioc-devel] BiocCheck and version requirement

[Kern, Lori]

>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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