Improved documentation for quarto users (working directory, kableExtra, and warning messages)

[mitchellcameron123]

Hi,

First of all, thank you for making this outstanding package!

I am a quarto user and I have found a few issues that could be clarified in the documentation (hence I am putting this through as an idea). Perhaps these are "bugs" so I am happy to put through a bug report as well.

First, your documentation advises " It is recommended to set out.dir = getwd().". Running quarto render (in the terminal such as for publishing) will lead to an error. Perhaps the documentation should state that out.dir = tempdir() is required in this case. Regardless of quarto, I feel this should be clarified as the description in the help file (?cite_packages) states that getwd() is recommended by then the coded examples state tempdir().

Second, the kableExtra package does process the citations. This is a general problem in quarto and citations in tables here. Perhaps the package documentation could provide a workaround similar too:

#| output: asis
pkgs <- cite_packages(output = "table", tempdir())

kbl(pkgs, booktabs = T, align = "c") %>%
  kable_styling(full_width = T) %>%
  unclass() %>% cat()

Third, when a large number of packages are detected, the warning suggests that options(renv.config.dependencies.limit = Inf) is used. However, in quarto at least (perhaps other formats), this will lead to an error. The warning can be resolved by setting it to be sufficiently high instead of inf such asoptions(renv.config.dependencies.limit = 10000).

I hope these points are helpful for quarto users to be aware of in your documentation. I realise these may be niche cases, but additional documentation may save users some time figuring this all out.

Kind regards,

[Pakillo]

Discussion continued here: #50