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

[Uwe Ligges]

On 03.05.2023 23:00, Simon Urbanek wrote:
> 
> 
>> On May 4, 2023, at 3:36 AM, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
>>
>> CRAN is fine with Bioconductor Depends: and Imports: dependencies, as previously mentioned. This is because the CRAN maintainers explicitly configure their system to know about Bioconductor package repositories.
>>
> 
> That is not exactly true (at least not for all maintainers ;)). Bioconductor packages are installed on as-needed (best-effort) basis and it is a manual process.

Apparently for MacOS.
On Fedora/Debian/WIndows we auto install from BioC. (actually, on 
Windows all BioC software packages are preinstalled).

Best,
Uwe Ligges

> Ideally, Bioconductor packages would be in Suggests, because if they are not, the package binary will be effectively broken for most users as they cannot install it without additional steps (and no stable state can be guaranteed, either). That's why I believe someone was suggesting a pre-flight check that alerts the user to such situation and prints instructions to remedy it (e.g., to use setRepositories()) as the majority of users will have no idea what's going on.
> 
> Cheers,
> Simon
> 
> 
> 
>> Users face a different challenge -- many users will not have identified (e.g., via `setRepositories()` a Bioconductor repository, so when they try to install your package it will fail in a way that you have no control over -- a generic message saying that the Bioconductor dependencies was not found.
>>
>> You could mitigate this by advertising that your CRAN package should be installed via `BiocManager::install("<your CRAN package>")`, which defines appropriate repositories for both CRAN and Bioconductor, but there is no way to unambiguously communicate this to users.
>>
>> Martin
>>
>> From: R-package-devel <r-package-devel-bounces using r-project.org> on behalf of Ruff, Sergej <Sergej.Ruff using tiho-hannover.de>
>> Date: Wednesday, May 3, 2023 at 11:13 AM
>> To: Dirk Eddelbuettel <edd using debian.org>
>> Cc: r-package-devel using r-project.org <r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
>> Thank you, Dirk.
>>
>>
>> I see your dependencies are Suggested. I know that Suggested dependencies should be conditional.
>>
>>
>> Do you know if Non-Cran (Bioconductor) packages need to be conditional?  Do you have any experiece regarding Non-CRAN Dependencies
>>
>> and how to handle them?
>>
>>
>> I believe Duncan Murdoch's experience and opinion regarding that topic, but i take any second and third opinion to be sure.
>>
>>
>> Thank you for your help.
>>
>>
>> Sergej
>>
>> ________________________________
>> Von: Dirk Eddelbuettel <edd using debian.org>
>> Gesendet: Mittwoch, 3. Mai 2023 16:22:09
>> An: Ruff, Sergej
>> Cc: Duncan Murdoch; Ivan Krylov; 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
>>
>>
>> Sergej,
>>
>> Please consider:
>>
>>   - there are nearly 20k CRAN packages
>>
>>   - all of them are mirrored at https://github.com/cran so you can browse
>>
>>   - pick any one 'heavy' package you like, Seurat is a good example; there
>>     are other examples in geospatial or bioinformatics etc
>>
>>   - you can browse _and search_ these to your hearts content
>>
>> Here is an example of mine. In RcppArmadillo, years ago we (thanks to fine
>> Google Summer of Code work by Binxiang Ni) added extended support for sparse
>> matrices pass-through / conversione from R to C++ / Armadillo and back. That
>> is clearly an optional feature as most uses of (Rcpp)Armadillo use dense
>> matrices. So all code and test code is _conditional_.  File DESCRIPTION has
>>
>>    Suggests: [...], Matrix (>= 1.3.0), [...], reticulate, slam
>>
>> mostly for tests. I.e. We have very little R code: in one single file
>> R/SciPy2R.R we switched to doing this via reticulate and opee the function
>> with
>>
>>     if (!requireNamespace("reticulate", quietly=TRUE)) {
>>         stop("You must install the 'reticulate' package (and have SciPy).", call.=FALSE)
>>     }
>>
>> after an actual deprecation warning (as there was scipy converter once).
>>
>> Similarly, the testsuites in inst/tinytests/* have several
>>
>>     if (!requireNamespace("Matrix", quietly=TRUE)) exit_file("No Matrix package")
>>
>> as well as
>>
>>     if (!requireNamespace("reticulate", quietly=TRUE)) exit_file("Package reticulate missing")
>>
>>     if (!packageVersion("reticulate") >= package_version("1.14"))
>>         exit_file("SciPy not needed on newer reticulate")
>>
>> and tests for slam (another sparse matrix package besides the functionality
>> in Matrix).
>>
>> Hopefully this brief snapshot gives you an idea.  There are (likely!!)
>> thousandss of examples you can browse, and I am sure you will find something.
>> If you have further (concrete) questions please do not hesitate to use the
>> resource of this list.
>>
>> Cheers (or I should say "mit Braunschweiger Gruessen nach Hannover),
>>
>> Dirk
>>
>> --
>> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>>
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>>
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