[R-pkg-devel] R vignettes

[Danielle Maeser]

Hi Duncan,

I really appreciate your response. Unfortunately, I am still receiving the
error below.

If anyone has ideas, I'd appreciate it!

This is the only online forum I can find that discusses the error, but I
have not found it helpful: https://github.com/r-lib/cli/issues/94




*   ERROR: package installation failedError: 'col_ed' is not an exported
object from 'namespace:cli'Execution halted*

On Wed, Apr 28, 2021 at 7:32 PM Duncan Murdoch <murdoch.duncan using gmail.com>
wrote:

> 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
> >
>
>

-- 
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

	[[alternative HTML version deleted]]