detect tlmgr issue and refresh installation info

[cderv]

We start seeing in our CI

compilation failed- tlmgr needs to be updated, but the update failed
    LaTeX Error: Mismatched LaTeX support files detected.
    (LaTeX)        Loading 'expl3.sty' aborted!
    (LaTeX)        
    (LaTeX)        The L3 programming layer in the LaTeX format
    (LaTeX)        is dated [202](https://github.com/quarto-dev/quarto-cli/actions/runs/6547127605/job/17779023801#step:25:203)3-08-29, but in your TeX tree the files require
    (LaTeX)        at least 2023-10-10.
    
    For immediate help type H <return>.

This is a know issue that requires some refreshing. We have seen the issue with tinytex

• Mismatched LaTeX support files detected rstudio/tinytex#424

We probably need to implement the same detection and commands to run.

[yihui]

FYI I have tried TinyTeX v2023.10 on macOS to render plos and jss templates in Quarto, but was unable to reproduce the problem. I'll see if it's possible to reproduce the problem on Ubuntu.

[kompre]

I've got that error message on my windows machine, that run quarto 1.3.450. I am not sure how to fix that on my windows machine (I don't use/have Rstudio)

[mcanouil]

I got it on macOS but before the issue was open so cannot really reproduce.
At that time I was running the september version of TinyTex.

@kompre The following should solve the issue, assuming you installed TinyTex using Quarto.

quarto update tinytex

[cderv]

As described in rstudio/tinytex#424 the issue is more complex than that, and updating may (or may not) solve the issue. Our CI runs was failing with the latest TinyTeX install using quarto from october. And now more issue.... So not sure to understand what is causing it. (maybe an order of updating packages.... 🤔 )

Anyhow, using TinyTeX daily builds is the best way to avoid this. We are still looking on how to correctly detect and help fix this.
(which would be automatically running in Quarto, the equivalent from R world which is tinytex:::refresh_all())

[kompre]

I got it on macOS but before the issue was open so cannot really reproduce. At that time I was running the september version of TinyTex.

@kompre The following should solve the issue, assuming you installed TinyTex using Quarto.

quarto update tinytex

thanks, this worked

[cderv]

Awesome. Good to know !

But this makes this issue even less reproducible 😞 - really not sure what is happening. We'll leave that open an see if it happens again

[yihui]

I have also tried on Ubuntu and was still unable to reproduce the problem. It's really odd. It seems that this problem has also gone in GHA: https://github.com/quarto-dev/quarto-cli/actions/workflows/test-smokes-parallel.yml?query=branch%3Amain

[yihui]

I have finally figured out how to reproduce this problem. I think it was caused by Quarto's lack of running fmtutil-sys, which was done in the R package tinytex via rstudio/tinytex@5946a2a. In tinytex, before installing a missing LaTeX package, I'll check if it has already been installed (in this case, l3kernel). If it has, I'll run tinytex::tlmgr_update() first, which runs fmtutil-sys --all by default, which fixes the l3kernel version mismatch problem.

Running tlmgr update --all without fmtutil-sys --all should be the reason why TinyTeX got into a broken state, which also made it fail to render R Markdown documents. Although @wesleyburr reported that Quarto could be isolated from the problem (rstudio/tinytex#424 (comment)), I'm reasonably sure it was Quarto that first brought TinyTeX into a broken state.

I think it suffices to run fmtutil-sys. Other commands in tinytex::refresh_all() should be unnecessary to fix this problem.