[Bioc-devel] BiocCheck and version requirement
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 at gmail.com>
Sent: Thursday, April 8, 2021 1:33 PM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] BiocCheck and version requirement
Sent: Thursday, April 8, 2021 1:33 PM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel <bioc-devel at 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 at roswellpark.org<mailto:Lori.Shepherd at 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 at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Kasper Daniel Hansen <kasperdanielhansen at gmail.com<mailto:kasperdanielhansen at gmail.com>>
Sent: Thursday, April 8, 2021 9:44 AM
To: bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at 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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