[R-pkg-devel] R vignettes

[Gábor Csárdi]

That's not the _full_ output, unfortunately. And if you can't share a
file that reproduces this (not necessarily your original file!), then
Duncan's advice is all we can tell you: don't install packages in
vignettes.

Gabor

On Thu, Apr 29, 2021 at 7:34 PM Danielle Maeser <maese005 using umn.edu> wrote:
>
> 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 failed
>
> Error: 'col_ed' is not an exported object from 'namespace:cli'
> Execution halted
>
> Exited 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
>