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}
(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.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
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