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

Am 15.05.24 um 00:09 schrieb Llu?s 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}

(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,

Llu?s


On Tue, 14 May 2024 at 22:48, Li, Junhui <Junhui.Li11 at 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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