[R-pkg-devel] R vignettes

[Duncan Murdoch]

On 28/04/2021 4:41 p.m., Danielle Maeser wrote:
> Hi Duncan,
> 
> Thank you for your feedback!
> 
> Unfortunately, when I made the changes recommended I have a new error:
> 
> *trying to use CRAN without setting a mirror

That would be a result of your code.  Do you call install.packages() in 
one of your functions?  Normally you shouldn't do that.

> *
> 
> And:
> *Error: 'col_ed' is not an exported object from 'namespace:cli'*

Similarly, something in your code or NAMESPACE file.  Do you refer to 
cli::col_ed, or try to import col_ed from cli?

> *
> *
> My description file includes:
> *VignetteBuilder: knitr
> Depends: R (>= 4.0), knitr
> License: GPL-2
> Encoding: UTF-8
> Roxygen: list(rmarkdown = TRUE)
> RoxygenNote: 7.1.1
> LazyData: true

Do you really have a data subdir in your package? You shouldn't have the 
LazyData line without one.

> Suggests: knitr, rmarkdown*

You shouldn't list knitr in both Depends and Suggests.

Duncan Murdoch

> *
> *
> And my vignette includes:
> *title: "title"
> author: "name"
> output: rmarkdown::html_vignette
> vignette: >
>    %\VignetteIndexEntry{title}
>    %\VignetteEngine{knitr::rmarkdown}
>    %\VignetteEncoding{UTF-8}*
> *
> *
> I'd appreciate any advice!
> 
> Danielle
> 
> On Wed, Apr 28, 2021 at 2:27 PM Duncan Murdoch <murdoch.duncan using gmail.com 
> <mailto:murdoch.duncan using gmail.com>> wrote:
> 
>     On 28/04/2021 2:44 p.m., Danielle Maeser wrote:
>      > Hello,
>      >
>      > I am doing a R CMD check on an R package I have developed.
>     However, I keep
>      > receiving the warning below:
>      >
>      > *Files in the 'vignettes' directory but no files in 'inst/doc':*
>      >
>      > And
>      >
>      > *Files named as vignettes but with no recognized vignette engine:*
>      >
>      > I am pretty sure I have the correct YAML header for my vignettes,
>     and also
>      > inst/docs is an older convention for vignettes that's no longer
>      > recommended.
>      >
>      > Do you have an idea of what's going wrong? I have attached my
>     YAML header
>      > below as reference.
> 
>     You may be missing the line
> 
>         VignetteBuilder: knitr
> 
>     in your DESCRIPTION file.  Without that, R won't know how to interpret
>     your vignette.
> 
>     It's also a little unusual to use
> 
>         %\VignetteEngine{knitr::markdown}
> 
>     nowadays; the more common engine is knitr::rmarkdown (but I believe
>     both
>     are still supported).  If you make this change you should also have
> 
>         rmarkdown::html_vignette
> 
>     as the output format.
> 
>     Finally, since a recent update of knitr, you need to make sure that
>     package holding the output format (i.e. markdown currently,
>     rmarkdown if
>     you make the change above) is declared as a Suggested package in your
>     DESCRIPTION file.
> 
>     Duncan Murdoch
> 
>      >
>      > Sincerely,
>      > Danielle
>      >
>      >
>      >
>      >
>      >
>      >
>      >
>      > *title: "title of this vignette"author: "name"output:
>      > markdown::html_vignettevignette: >  %\VignetteIndexEntry{vignette
>     title}
>      > %\VignetteEngine{knitr::markdown}  %\VignetteEncoding{UTF-8}*
>      >
> 
> 
> 
> -- 
> Ph.D. Student
> Bioinformatics and Computational Biology
> University of Minnesota
>