Am 16.05.24 um 11:34 schrieb Duncan Murdoch:
On 2024-05-16 4:15 a.m., 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.
It is documented in WRE as a soft dependency of the package: "As Sweave
is the only engine supplied with the R distribution, the package
providing any other engine must be specified in the ‘VignetteBuilder’
field of the package DESCRIPTION file, and also specified in the
‘Suggests’, ‘Imports’ or ‘Depends’ field (since its namespace must be
available to build or check your package)."
I forget now, but presumably the thinking at the time was that Suggested
packages would always be available for building and checking vignettes.
With most soft dependencies, it's up to the package writer to handle the
possibility that it is missing, but here, I think it has to be the check
code that does it, skipping the vignette test if the builder is missing.
Yes, re-building vignettes is skipped when a VignetteBuilder package is
unavailable.
In the present case, the VignetteBuilder package that provides the
engine is knitr and BiocStyle is used for an alternative rmarkdown
output format. Not sure if the latter should be declared as an
additional VignetteBuilder even if it does not provide the vignette
engine, but you are right that it comes very close.
Alternatively, it could be required to be a hard dependency, but that
seems too strong: most package users don't need to rebuild vignettes.
Agreed. Declaring it as part of the vignette's \VignetteDepends is what
I'd do to solve the check issue.
Sebastian Meyer
Duncan Murdoch
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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