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

[Lluís Revilla]

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.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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>
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