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 <maese...@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.ga...@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 <maese...@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.dun...@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.dun...@gmail.com >> > > > <mailto:murdoch.dun...@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@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > -- > Ph.D. Student > Bioinformatics and Computational Biology > University of Minnesota > ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
