TIL, with the drop of pandoc 3.0 that RStudio installs its own version of pandoc in /Applications/RStudio.app/Contents/Resources/app/quarto/bin And, in the subdirectory tools other binaries that I have already installed.
I think I've reached the tipping point that the only way forward is to switch to RStudio Server running in a virtual ubuntu, maybe in docker. That or VSCode, if it's not giving me two watches with which to be uncertain what time it is.
@technocrat Pandoc is shipped with RStudio IDE since a long time. Nothing to do with Pandoc 3.0
Since a few version of RStudio IDE, and since Quarto v1 is out probably, Quarto is shipped with RStudio IDE too. As Quarto bundles Pandoc itself, RStudio IDE is now using the Pandoc version shipped with Quarto.
Latest version of RStudio IDE should use Quarto binary found on PATH, and if none, it will be using the bundled version.
Regarding Pandoc,
Quarto will always use the Pandoc version it is shipping (because a Quarto version only works with a specific Pandoc version).
If only Pandoc is necessary, like with rmarkdown::render(), the detection process of rmarkdown is to use the pandoc binary with higher version from PATH or the one bundle in RStudio IDE.
Anyway, I am surprised you don't get the same result in CLI and IDE:
Which version of the IDE are you using ?
Can you do quarto check install inside your Terminal and inside RStudio IDE's terminal ?
And here is what will happen when the Elspeth looks in $PATH for quarto
> Sys.which("quarto")
quarto
"/Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto"
> system("quarto check")
/Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto: line 19: dirname: command not found
/Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto: line 23: basename: command not found
ERROR: Cannot determine the Quarto source path. This script must be run from the bin or common folder.
All of this implicates something evil done to ignore $PATH, leading, of course, to
install.packages("A3")
#> also installing the dependency 'pbapply'
#> Warning in system(paste0("tar zxf \"", path.expand(what), "\" -C \"",
#> path.expand(where), : error in running command
#> Warning: 'tar' returned non-zero exit code 127
#> Error: file '/var/folders/0j/3g7q2zss7fb55q5wqg9t141r0000gn/T//RtmpbnuOm1/downloaded_packages/pbapply_1.7-0.tgz' is not a macOS binary package
and with update.packages(). Wrong $PATH means no tar means no unzip, which means no install.
Thanks for sharing - we've got a bit off track for original issue though.
I don't understand this would error. quarto is found as the one bundled in IDE, so next command should work; Somehow this is broken. Check your IDE version and maybe update to more recent one if not already. Latest version is recommended with Quarto.
It seems like you have a independant quarto on PATH - this is good and should have been found and used by IDE. Again not sure what is wrong, except not latest version.
Please do open issues in RStudio IDE if you get the same with latest version.