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

[Simon Urbanek]

Sharon,

I have upgraded Bioc on the R-oldrel build machines and that seems to have 
taken care of the problem as far as I can tell:
https://cran.r-project.org/web/checks/check_results_HybridMicrobiomes.html

If you have reports like that, it's a better idea to ask us first and always 
supply the name of the package, otherwise the thread can quickly degrade to 
wild guesswork and misleading or incorrect answers from unrelated parties.

Cheers,
Simon


> On 7/05/2024, at 6:56 PM, Simon Urbanek  wrote:
> 
> 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
> 

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [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  wrote:
> 
> On Tue, 7 May 2024 10:07:59 +1200
> Simon Urbanek  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
> 

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

[Ivan Krylov via R-package-devel]

On Tue, 7 May 2024 10:07:59 +1200
Simon Urbanek  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

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [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 
>  wrote:
> 
> В Sat, 4 May 2024 15:53:25 +
> Sharon Bewick  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
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

[Ivan Krylov via R-package-devel]

В Sat, 4 May 2024 15:53:25 +
Sharon Bewick  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.

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

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

[Duncan Murdoch]

On 04/05/2024 11:53 a.m., Sharon Bewick wrote:

I’m having trouble with:
r-oldrel-macos-arm64 

and
r-oldrel-macos-x86_64 


flagging an error because 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? I feel like I had 
this problem with microViz in the past, but now it’s coming up with phylseq 
too, and I can’t remove that dependency.



phyloseq is a Bioconductor package. It appears to be available from 
BioConductor, so it doesn't matter that it's not on CRAN.


Have you tried submitting your package to CRAN?  If so, could you show 
us the error you received?


Duncan Murdoch

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

[Sharon Bewick]

I’m having trouble with:
r-oldrel-macos-arm64 

and
r-oldrel-macos-x86_64 


flagging an error because 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? I feel like I had 
this problem with microViz in the past, but now it’s coming up with phylseq 
too, and I can’t remove that dependency.

Thanks!
Sharon__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel