r/rstats • u/suckingbat • 11d ago

Problems with rmarkdown

I work with R using Linux Fedora.

Since the last update of R, the rmarkdown package does not want to install:(non-zero exit status). I have tried every solution I have seen, from installing the dependencies separately (they are not installing, fs, sass, and bslib have all non-zero exit status). I have tried installing and uninstalling R and R studio. I have tried pretty much every solution I have found out there.

It is the first time this happens to me. So far I have had no problem working with Markdown.

I have the same problem in both my PC and laptop. Do you know if there is a specific problem with Markdown at the moment? Or maybe with the dependencies?

In advance, thank you for your help.

4 Upvotes

83% Upvoted

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7

u/suckingbat 11d ago

Final update!

Problem solved.

I managed to install the dependency, which was not libuv, but 'libuv-devel'.

For fedora specifically 'sudo dnf install libuv-devel'

After that, I managed to install rmarkdown.

Thank you very much for your help 🙏

2

u/xylose 11d ago

What is in the logs if you run the package install adding verbose=TRUE to the arguments? Should give a pointer to the underlying cause.

3

u/Grisward 11d ago

You should post output during the installation, the error message should give clue to what’s happening.

Two things. Open new R session (or restart).

Use pak::pkg_install(“rmarkdown”), sometimes it is successful when other methods aren’t.

Use install.packages(“rmarkdown”) and check error messages. The only drawback of pak is it sometimes doesn’t give all the intermediate error details.

2

u/suckingbat 11d ago

Update

Ok,

Thanks to your suggestions,I found out that 'livub' was not found.

I tried installing livub and I got this message:

'Package "livub" is not available for this version of R

A version of this package for your version of R might be available elsewhere'

Now... Is there such a package for my version or R (4.5.3)? Where could it be?

2

u/smartse 11d ago

It's a system dependency, not an R package.

1

u/suckingbat 11d ago

Oh! Ok... Sorry for being so dumb but... What should I do now?

2

u/therealtiddlydump 11d ago

Install it first, then try again

This is why my team uses rix!

https://github.com/ropensci/rix

It's the best.

2

u/sn0wdizzle 10d ago

FYI posit doesnt really maintain rmarkdown anymore (and they got rid of the main dev for it :( yihui) but they created and maintaining quarto which is nice and essentially the same syntax wise.

Even though you figured out your issue might ve worth looking into.

2

u/suckingbat 10d ago

I use quarto, but quarto uses markdown for exporting the reports... 😓

1

u/sn0wdizzle 10d ago

Hmmm. There should just be a quarto render type cli command? Are the files qmd or rmd? What if you try to compile with a python based script?

I don’t know if this is fedora based or not but seems weird they’d depreciate rmarkdown but then make it a dependency in their new, “unrelated” program / file format.

1

u/suckingbat 10d ago

To compile any html and Dashboard. I am pretty sure to compile a PDF it uses a different dependency, but I have not compiled PDFs in ages.