[R-pkg-devel] R vignettes

[Gábor Csárdi]

If you could share a reproducible example with us, and/or you could
show the full output, then we could probably help you better.

Gabor

On Thu, Apr 29, 2021 at 6:29 PM Danielle Maeser <maese005 using umn.edu> wrote:
>
> 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
>
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>
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