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

[Ruff, Sergej]

my bad,


I looked at the DESCRIPTIOn fiel again. I assumed that Cluster was a Bioconductor package.

I also didn�t see that DeSeq2 was in Suggests.


I will follow your advice and try using Bioconductor packages without a conditional function.


Sergej

________________________________
Von: Duncan Murdoch <murdoch.duncan using gmail.com>
Gesendet: Mittwoch, 3. Mai 2023 17:25:15
An: Ruff, Sergej; Ivan Krylov
Cc: r-package-devel using r-project.org
Betreff: Re: AW: AW: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On 03/05/2023 9:50 a.m., Ruff, Sergej wrote:
> I took the Seurat package as an example, because it both lists the
> Bioconductor Dependencies under Imports in the DESCRIPTION-File

Which packages are you talking about?  I don't see any BioConductor
dependencies in the Imports list for the current Seurat version.

Duncan Murdoch

>
> 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/
> <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/
> <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/
> <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
>>
>


	[[alternative HTML version deleted]]