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

[Uwe Ligges]

On 16.05.2024 10:15, Sebastian Meyer wrote:
> Am 15.05.24 um 00:09 schrieb 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).
> 
> Yes, I'd consider the package providing the vignette output format for 
> the rmarkdown engine, here BiocStyle, as a strong dependency of that 
> vignette. The error from the additional "noSuggests" check 
> (<https://www.stats.ox.ac.uk/pub/bdr/noSuggests/README.txt>) shows it 
> cannot be rebuild if BiocStyle is unavailable.
> 
> The 'StepReg' vignette could use a metadata line to declare strong 
> vignette dependencies, for example:
> 
>      %\VignetteDepends{StepReg, BiocStyle, kableExtra}

Indeed, having it listed in Suggests plus the \VignetteDepends 
declaration should suffice.

Best,
Uwe Ligges



> 
> (I haven't checked if this list is complete.)
> 
> This avoids spurious check errors in incomplete setups, such as when 
> mass-checking packages (e.g., reverse dependencies) without some of the 
> suggested packages being installed.
> 
> Best,
> 
>      Sebastian Meyer
> 
>>
>> 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
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>
>>     [[alternative HTML version deleted]]
>>
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