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.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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