[R-pkg-devel] Trouble with dependencies on phyloseq and microViz

[Simon Urbanek]

Ivan,

sorry if it wasn't clear, but this thread was about strong dependencies -- Sharon noted that phyloseq must remain strong dependency and asked how to deal with that (see all the parts you cut from this thread). Now that I finally have the package name I can check the details - apparently this only affects R-oldrel so presumable Bioc upgrade may fix this so I'll have a look tomorrow.

Cheers,
Simon



> On May 7, 2024, at 6:15 PM, Ivan Krylov <ikrylov using disroot.org> wrote:
> 
> On Tue, 7 May 2024 10:07:59 +1200
> Simon Urbanek <simon.urbanek using R-project.org> wrote:
> 
>> That doesn't work - additional repositories are not allowed on CRAN
>> other than in very exceptional cases, because it means the package
>> cannot be installed by users making it somewhat pointless.
> 
> I suppose that with(tools::CRAN_package_db(),
> sum(!is.na(Additional_repositories)) / length(Additional_repositories))
> = 0.7% does make it very rare. But not even for a weak dependency? Is
> it for data packages only, as seems to be the focus of
> [10.32614/RJ-2017-026]? The current wording of the CRAN policy makes it
> sound like Additional_repositories is preferred to explaining the
> non-mainstream weak dependencies in Description.
> 
> So what should be done about the non-Bioconductor weak dependency
> microViz?
> 
>> As for the OP, can you post the name of the package and/or the link
>> to the errors so I can have a look?
> 
> Sharon has since got rid of the WARNING and now only has NOTEs due to
> microViz and a URL to its repo in the Description:
> https://win-builder.r-project.org/incoming_pretest/HybridMicrobiomes_0.1.2_20240504_185748/Debian/00check.log
> 
> If Additional_repositories: is the correct way to specify a
> non-mainstream weak dependency for a CRAN package, the URL must be
> specified as https://david-barnett.r-universe.dev/src/contrib, not just
> https://david-barnett.r-universe.dev/. I am sorry for not getting it
> right the first time.
> 
> -- 
> Best regards,
> Ivan
>