[R-pkg-devel] R vignettes

[Danielle Maeser]

Hi Gabor,

My full output is below:









*   Error: object 'col_ed' is not exported by 'namespace:cli'   Execution
halted   ERROR: lazy loading failed for package 'packagename'
 -----------------------------------   ERROR: package installation
failedError: 'col_ed' is not an exported object from
'namespace:cli'Execution haltedExited with status 1.*

Unfortunately, I can't share a full reproducible example since this package
is also included in a manuscript for publication.

I don't export any objects named 'col_ed' so I am quite perplexed by this
error message.

I'd appreciate any advice!

Danielle

On Thu, Apr 29, 2021 at 11:42 AM Gábor Csárdi <csardi.gabor using gmail.com>
wrote:

> 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
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>


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

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