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

[Simon Urbanek]

> On 5/05/2024, at 4:32 AM, Ivan Krylov via R-package-devel <r-package-devel using r-project.org> wrote:
> 
> В Sat, 4 May 2024 15:53:25 +0000
> Sharon Bewick <sbewick using clemson.edu> пишет:
> 
>> I have a dependency on phyloseq, which is available through GitHub
>> but not on the CRAN site. I have a similar problem with microViz,
>> however I’ve managed to make it suggested, rather than required.
>> There is no way to get around the phyloseq requirement. How do I fix
>> this problem so that I can upload my package to the CRAN website?
> 
> Did a human reviewer tell you to get rid of the dependencies? There is
> at least 444 packages on CRAN with strong dependencies on Bioconductor
> packages, so your phyloseq dependency should work. In fact, 14 of them
> depend on phyloseq.
> 
> What you need is an Additional_repositories field in your DESCRIPTION
> specifying the source package repository where microViz could be
> installed from. I think that
> 
> Additional_repositories: https://david-barnett.r-universe.dev
> 
> ...should work.
> 

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. Bioconductor doesn't need to be flagged in Additional_repositories, but not all packages are available - only those that do no depend on the data repository.

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?

Cheers,
Simon



> Besides that, you'll need to increment the version and list the *.Rproj
> file in .Rbuildignore:
> https://win-builder.r-project.org/incoming_pretest/HybridMicrobiomes_0.1.1_20240504_173331/Debian/00check.log
> 
> -- 
> Best regards,
> Ivan
> 
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