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

I am currently building a package which uses the "limma"-package as a dependency. I want to submit my package to CRAN. Do I need to declare Bioconductor-dependencies such as Limma differently in the Description-File of my Package? The Check-Function in R shows no Notes, Warnings or Errors, but

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

В Thu, 16 Mar 2023 11:09:16 + "Ruff, Sergej" пишет: > The Check-Function in R shows no Notes, Warnings or Errors, but I am > not sure if that means that limma will install when installing my > package from CRAN. > Currently I am declaring limma like this: > > Suggests: > > limma insta

[R-pkg-devel] Should 'methods' be in Imports?

Hello developers, I am wondering if base packages whose functions are used in my package need to be present in Imports in my DESCRIPTION. For example, if I use the function abline(), which exists in the *graphics* package, do I need to include *graphics* in Imports? Note I am not asking about whet

Re: [R-pkg-devel] Should 'methods' be in Imports?

I think the Writing R Extensions manual is pretty clear about this: yes, you should include "methods" in Imports or Depends if you are calling methods::. You say "some packages do so and some don't". Which ones don't? It's helpful to be specific in your examples. Duncan Murdoch On 16/03/2

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

Hi, My package pliman depends on EBImage which is in Bioconductor. I have created a function check_ebi() < https://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534> that is called in .onAttach() < https://github.com/TiagoOlivoto/pliman/blob/master/R/zz

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

thank you. I see you added biocView: below your suggested Dependencies. Is it necessary for CRAN to identify Bioconductor Dependencies and if so, should I add it below or above the suggested packages? Do I also need BiocManager among my Suggests? Last question: How does CRAN work with Biocond

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

On 16/03/2023 12:36 p.m., Tiago Olivoto wrote: Hi, My package pliman depends on EBImage which is in Bioconductor. I have created a function check_ebi() < https://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534> that is called in .onAttach() < https:

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

Hi Sergej, I sincerely don't know if the position of biocView really matters (I'll try it when preparing for the new CRAN release of pliman). I believe that biocView will not allow you to put limma in the imports field and automatically install it from Bioconductor, as you can see here in this dis

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

Thanks Duncan, I'm in the way of a new CRAN submission and I will make sure to call check_ebi() in the body of each function. This should ensure that the check for EBImage will be called even with pliman::object_edge( ... ), for example. Best regards, Olivoto Em qui., 16 de mar. de 2023 às 14:15,

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 + "Ruff, Sergej" 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

Re: [R-pkg-devel] Should 'methods' be in Imports?

Thank you for your input. *broom*, *mlogit*, *twang*, and *Hmisc* are examples of major packages that import functions from *stats*, *utils*, *graphics*, or other base packages but don't include them in the DESCRIPTION. All of my packages (*cobalt*, *WeightIt*, *MatchIt*) do too, and I have never h

Re: [R-pkg-devel] Should 'methods' be in Imports?

On 16/03/2023 2:21 p.m., Noah Greifer wrote: Thank you for your input. /broom/, /mlogit/, /twang/, and /Hmisc/ are examples of major packages that import functions from /stats/, /utils/, /graphics/, or other base packages but don't include them in the DESCRIPTION. All of my packages (/cobalt/

Re: [R-pkg-devel] Should 'methods' be in Imports?

On Thu, 16 Mar 2023 11:29:33 -0400 Noah Greifer wrote: > Is including these packages filling the DESCRIPTION with unnecessary > dependencies that are automatically satisfied, or is it being > helpfully explicit about the packages your package relies on? Here's a comment from the part of R CMD ch

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 inst

Re: [R-pkg-devel] Should 'methods' be in Imports?

Thank you both for your responses. Based on Ivan's dig into the comments, it seems there is ambiguity, even by the CRAN team. Still, it looks like it would be preferable to (and would not cause any harm to) include the base packages in DESCRIPTION if they are used at all in a package, whether by ::