[R-pkg-devel] CRAN packages dependency on bioconductor packages

[Li, Junhui]

Hi Llu�s,

Thanks for your input. I believe it is ok to use a vignette output conditionally with knitr. However,  what confuses me is that I was able to successfully upload StepReg version 1.5.0 to CRAN with BiocStyle listed in the Suggests field. It seems that there is some issues with CRAN check.

Best,
Junhui
From: Llu�s Revilla <lluis.revilla using gmail.com>
Date: Tuesday, May 14, 2024 at 18:09
To: Li, Junhui <Junhui.Li11 using umassmed.edu>
Cc: r-package-devel using r-project.org <r-package-devel using r-project.org>
Subject: Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages
Hi Junhui,

There is a separate log for checking if your package works without suggested packages: in the StepReg results
The noSuggests title leads to: https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out
Where you can see that it fails if a user don't have BiocStyle installed.
I don't know if it is possible to use a vignette output conditionally with knitr: In any case it seems that it would be a requirement (Imports, or Depends).

However, it is best to not use the Bioconductor style for a package in CRAN.
You could use the *_vignette or *_document format directly (from rmarkdown if I recall correctly).
You will remove a dependency and avoid this problem entirely.

Best,

Llu�s


On Tue, 14 May 2024 at 22:48, Li, Junhui <Junhui.Li11 using umassmed.edu<mailto:Junhui.Li11 using umassmed.edu>> wrote:
Hi everyone,

I recently developed an R package called 'StepReg' and used the Bioconductor R package 'BiocStyle' in my vignettes, as shown below:

output:
  BiocStyle::html_document:
    toc_float: true
  BiocStyle::pdf_document: default

In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and included a new line 'biocViews:', as follows:

VignetteBuilder: knitr
biocViews:
Suggests:
    knitr,
    testthat,
    BiocStyle,
    kableExtra

You may find all those information here: https://github.com/JunhuiLi1017/StepReg/tree/dev

There were no error messages when checking with 'R CMD check' and on https://win-builder.r-project.org/upload.aspx. However, an error message occurred when I attempted to upload it to CRAN:

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'StepReg.Rmd' using rmarkdown
Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building 'StepReg.Rmd'

SUMMARY: processing the following file failed:
   'StepReg.Rmd'

Error: Vignette re-building failed.
Execution halted

For version 1.5.0 (https://cran.r-project.org/web/packages/StepReg/index.html), I successfully uploaded it to CRAN without including 'biocViews:' in the DESCRIPTION file two months ago. However, I'm encountering difficulties this time. Any insights or suggestions on resolving this issue would be greatly appreciated.

Thanks,
Junhui

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