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.revi...@gmail.com> Date: Tuesday, May 14, 2024 at 18:09 To: Li, Junhui <junhui.l...@umassmed.edu> Cc: r-package-devel@r-project.org <r-package-devel@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.l...@umassmed.edu<mailto:junhui.l...@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 [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]]
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