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, Lluís On Tue, 14 May 2024 at 22:48, Li, Junhui <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 mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
