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

[Ruff, Sergej]

I was wondering how CRAN will handle Limma when running the automatic check.


I am worried that my package will be rejected if Limma won�t install from Bioconductor on a clean version of R. Leading to an Error and Note during the check.


I am using Limma only for an example in my functions description, not inside my actual function.


How would CRAN�s System handle that when checking my package for submission?


with regards,


Sergej

________________________________
Von: Martin Morgan <mtmorgan.bioc using gmail.com>
Gesendet: Donnerstag, 16. M�rz 2023 20:12:51
An: Ivan Krylov; Ruff, Sergej
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

I would not follow the instructions in RTIGER�s README for installing Bioconductor packages.

BiocManager::install(�RTIGER�) would install both CRAN and Bioconductor dependencies of RTIGER, and would be my preferred instruction in a README or INSTALL file. A complete instruction might be to install your package as if it were on Bioconductor �

If (!requireNamepace(�BiocManager�, quietly = TRUE))
    install.packages(�BiocManager�)
BiocManager::install(�<your package>�)

It does not make sense to me to have instructions in .onAttach / .onLoad or in each function for the user to install a �Suggests:� package, when actually the package is required for use and belongs in Imports: or perhaps Depends:.

The instruction to use �version = �3.14�� of Bioconductor in the RTIGER document is not universally correct, since different Bioconductor versions are tied to specific R versions (see https://bioconductor.org/about/release-announcements/ ). On one version of R I am currently using, I get

> BiocManager::install(version = "3.14")
Error: Bioconductor version '3.14' requires R version '4.1'; use
  `BiocManager::install(version = '3.17')` with R version 4.3; see
  https://bioconductor.org/install

The instruction to install a vector of Bioconductor packages is also unnecessary for Bioconductor packages in the Imports: or Depends: field of <your package>, or if one were to pass the argument `dependencies = TRUE` to either BiocManager::install() or install.packages() (to get the Suggests: packages of <your package> to be installed, as well as Depends:, Imports: and LinkingTo:).

Briefly, installation requires R to know the correct repositories. The command

BiocManager::repositories()

Returns a vector of Bioconductor and CRAN repositories relevant to your version of R. If one is averse to using BiocManager::install(�RTIGER�), a reasonable alternative, though still requiring that the BiocManager package is installed, is

install.packages(�RTIGER�, repos = BiocManager::repositories())

Base R also provides a mechanism for specifying Bioconductor repositories, via `setRepositories()` called before install.packages(). However, this is not recommended because, as can be seen on the web page mentioned above, there are two versions of Bioconductor for each version of R � one always gets the �old� Bioconductor version, even when a newer version is available.

From: R-package-devel <r-package-devel-bounces using r-project.org> on behalf of Ivan Krylov <krylov.r00t using gmail.com>
Date: Thursday, March 16, 2023 at 2:15 PM
To: Ruff, Sergej <Sergej.Ruff using tiho-hannover.de>
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
On Thu, 16 Mar 2023 17:01:55 +0000
"Ruff, Sergej" <Sergej.Ruff using tiho-hannover.de> wrote:

> Last question: How does CRAN work with Bioconductor Dependencies?
> Will CRAN accept limma as a dependency or will my submission be
> rejected?

It's not explicitly spelled out in the CRAN policy
<https://cran.r-project.org/web/packages/policies.html>, but
Bioconductor and CRAN are the "mainstream repositories" for the
purposes of the following rule:

>> Packages on which a CRAN package depends should be available from a
>> mainstream repository

(Even non-mainstream repositories are allowed for optional dependencies
if you follow a few additional rules.)

Here's an example of a CRAN package with a strong dependency on a
Bioconductor package: <https://CRAN.R-project.org/package=RTIGER>. You
can see the extra instructions for installing the Bioconductor
dependencies in its README.

--
Best regards,
Ivan

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