How do I get Quarto to work with R in Ubuntu?

[ThomasA]

I have installed Quarto in Ubuntu from https://github.com/quarto-dev/quarto-cli/releases/download/v1.1.189/quarto-1.1.189-linux-amd64.deb. I can run quarto --help afterwards.
I try quarto preview on the template file https://github.com/WarwickCIM/quarto-workshop/blob/main/cases/template/documentation_template.qmd. This complains:

Error: 'hooks_markdown' is not an exported object from 'namespace:knitr'

I have absolutely no experience with R, but I believe I have installed it. I have installed the packages "r-base" and "r-cran-rmarkdown" from the default Ubuntu repositories, using apt. apt reports that I also have "r-cran-knitr" installed (probably a consequence of "r-cran-rmarkdown").

I can enter R and run the command library("knitr") with no errors, so I assume knitr looks installed from R's perspective.

Does anyone have any idea how to get this to work?

[cderv]

Can you share which version of knitr has been installed using the default Ubuntu repo ?

The function not found has been added in knitr 1.30 (https://github.com/yihui/knitr/blob/master/NEWS.md#changes-in-knitr-version-130)

I wonder if you have an older version somehow 🤔

Instruction to install R on Ubuntu can be found on CRAN website: https://cran.r-project.org/bin/linux/ubuntu/fullREADME.html

Hope it helps

[ThomasA]

I cannot seem to install R according to https://cran.r-project.org/bin/linux/ubuntu/fullREADME.html#installation because the repository does not seem to be signed. At least I cannot find instructions on where to get the signature from. Instructions for adding apt repositories in Ubuntu usually come with a command for importing the repository's signature.

[eitsupi]

R on Ubuntu is really hard and I don't think it is possible for a beginner to build an environment.

I think the easy way for now is to use a package-installed Docker container or use r2u. (cc @eddelbuettel)
https://github.com/eddelbuettel/r2u

[eitsupi]

I cannot seem to install R according to cran.r-project.org/bin/linux/ubuntu/fullREADME.html#installation because the repository does not seem to be signed. At least I cannot find instructions on where to get the signature from. Instructions for adding apt repositories in Ubuntu usually come with a command for importing the repository's signature.

I believe the following page linked from the R project describes it.
https://cran.r-project.org/bin/linux/ubuntu/

[ThomasA]

Thank you, that was exactly what I needed. I got confused by thinking https://cran.r-project.org/bin/linux/ubuntu/fullREADME.html#installation was where I needed to look, but the description at https://cran.r-project.org/bin/linux/ubuntu/ solves everything.

[cderv]

Good to know. Sorry to have pointed to the wrong page in the first place... 😞 Thanks @eitsupi !

[eddelbuettel]

Which Ubuntu version is this, and are you keeping CRAN up-to-date?

I am on 22.04, and have zero issues. Also see https://dirk.eddelbuettel.com/blog/2022/01/31#035_apt_install_rstudio_quarto -- I now use quarto (and the two RStudio packages) off a 'truly personal PPA' as I got tired of dealing with outside of the (usually daily) apt upgrades. That repo updates twice a week, and I happen to have gotten a new quarto package today. (I cannot make the repo public as the files are larger than what GitHub allows so 😞 the actual repo is local on my box.)

[ThomasA]

I am still on 20.04 and do not know what keeping CRAN up to date means. Maybe it is finally time to upgrade to 22.04...

[ThomasA]

#2333 (reply in thread) solved everything - wonderful 🥇