[R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

[Ruff, Sergej]

I took the Seurat package as an example, because it both lists the Bioconductor Dependencies under Imports in the DESCRIPTION-File

and it uses conditional functions to check if those dependencies are pre-installed.


"No, it is a requirement if the package is used but is not listed in
Depends or Imports.

If the package is in Depends or Imports it is a waste of time to make
the check:  it will always succeed."


that's what I also thought but I am confused why a package like Seurat then lists the dependencies in the DESCRIPTION-File and on top of that uses

conditional functions to check if the package is pre-installed or not. Wouldn't that make the packagecheck function used by Seurat redundant?

Sergej Ruff

________________________________
Von: Duncan Murdoch <murdoch.duncan using gmail.com>
Gesendet: Mittwoch, 3. Mai 2023 15:29:34
An: Ruff, Sergej; Ivan Krylov
Cc: r-package-devel using r-project.org
Betreff: Re: AW: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On 03/05/2023 9:17 a.m., Ruff, Sergej wrote:
> Thanks,
>
>
> So is it just necessary for suggested packages.

Those and "Enhances" packages, but hardly anyone uses "Enhances".
>
>
> So, is it just good practice to make a conditional check?

No, it is a requirement if the package is used but is not listed in
Depends or Imports.

If the package is in Depends or Imports it is a waste of time to make
the check:  it will always succeed.

> I saw some packages still include it.
>
>
> For example the Seurat package.
>
I don't understand your question here.

Duncan Murdoch

>
> Under Utils.R (line 349-379) of the SeuratObject-Package
> (https://cran.r-project.org/src/contrib/Archive/SeuratObject/
> <https://cran.r-project.org/src/contrib/Archive/SeuratObject/>) you will
> find the PackageCheck-function
>
> which used by the Seurat-Package
> (https://cran.r-project.org/src/contrib/Archive/Seurat/
> <https://cran.r-project.org/src/contrib/Archive/Seurat/>) to check if
> packages are alredy installed.
>
>
> You can find examples for DEseq2 under differential_expression.R
> (starting line 1314 or you cntr+f for packagecheck) in
> the Seurat.package
> (https://cran.r-project.org/src/contrib/Archive/Seurat/
> <https://cran.r-project.org/src/contrib/Archive/Seurat/>)
>
> or for limma (starting line 2292).
>
>
>
> ------------------------------------------------------------------------
> *Von:* Duncan Murdoch <murdoch.duncan using gmail.com>
> *Gesendet:* Mittwoch, 3. Mai 2023 14:25:56
> *An:* Ruff, Sergej; Ivan Krylov
> *Cc:* r-package-devel using r-project.org
> *Betreff:* Re: [R-pkg-devel] How to declare Bioconductor Dependencies in
> the Description File of my R Package
>
>
> On 03/05/2023 8:00 a.m., Ruff, Sergej wrote:
> ... [ lines about current solution deleted ]
>
>> Also for the future - how Do i provide Bioconductor dependencies as "Imports" for a package that I want to submit to CRAN?
>
> Just list it as you would a CRAN package.  The CRAN docs talk about
> "mainstream repositories"; I forget what the definition is of that
> (maybe repositories listed in `file.path(R.home(),
> "etc/repositories")`?), but definitely BioConductor is included.
>
>> Do I need to make that also conditional? I know I should provide Installation description in a readme fiel but how do I make sure
>
> No, you don't need to check.  If any imported package is not available,
> your package will not load, so errors will happen before you ever get to
> running examples.
>
>> that the Bioconductor dependencies dont cause a rejection from CRAN?
>
> Just make sure they exist on BioC and your code works with them.
>
> Duncan Murdoch
>


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