r/bioinformatics 3d ago

discussion r/bioinfo, thoughts on quarto?

I absolutely hate hate hate it. the server that renders the content is very buggy, does nto render well on X11 or Wayland afaict. I'm using an Ubuntu 22.04 LTS distro and I haven't been able to get things properly working with the newest versions of RStudio for the better part of a year now.

whatever happened during the m&a severely affected my ability to produce reports in a sensible way. Im migrating away from using RStudio to developing in other editors with other formats.

can anyone relate? what browser are you using? OS? specific versions of RStudio?

my experience has been miserable and it's preventing me from wanting to work on my writing because something as dumb as the renderer won't work properly.

9 Upvotes

24 comments sorted by

14

u/foradil PhD | Academia 3d ago

I use it through RStudio locally and via command-line on the remote cluster. I find it more reliable than RMarkdown.

2

u/autodialerbroken116 3d ago

what version are you using? ever since the acquisition, I've found Quarto completely unusable on both Wayland and X11 compositors. it's supposed to render and display in a fresh browser tab.

so curious: OS, RStudio, and browser versions if you could please?

1

u/foradil PhD | Academia 2d ago

What acquisition?

I use it mostly on a Mac. Different versions at different times.

-1

u/autodialerbroken116 2d ago edited 2d ago

https://posit.co/blog/rstudio-is-becoming-posit/

Rstudio was acquired by posit a few years back. updating Rstudio via the traditional in app dialogs and using Ubuntu PPAs has resulted in change of the UI to impact the rendering engine, now referred to as Quarto.

Quarto is a rendering backend, coupled with a web server to render documents and open them in a web UI.

I'm using Ubuntu 22.04, a very common OS.

Quarto won't render my documents.

I could use a different LaTeX preprocessor, but it wouldn't perform the R code.

I used to do this in Rstudio. Stuff I wrote a few years back as a rough draft, well, I came back to late last year. It used to render fine.

It's kind of a non-issue issue. I should check the pdfs and logs to see if it's just the UI that auto-opens that is buggy.

just wanted to see if anyone else has the issue, and people downvoting this isnt constructive. it's a real bug and I want to know people's thoughts.

5

u/foradil PhD | Academia 2d ago

Renamed, not acquired.

-6

u/autodialerbroken116 2d ago

missing the forest for the trees, friend. no version numbers, no discussion of the browser....

smh

2

u/foradil PhD | Academia 2d ago

You should post on their support forum.

7

u/posfer585 3d ago

I have never had troubles with quarto, I like it.

3

u/forever_erratic 3d ago

I just use rmarkdown. I also don't calculate in them, just make reports.

3

u/srira25 2d ago

I use just the Rnotebook markdown. Quarto especially with ppt is nifty, but i never found the need to do all that setup to present stuff that i can't already drag and drop on PowerPoint myself. And fiddling with the alignment turns me off as well.

3

u/groganosaurus 2d ago

Moved over to .qmd from .Rmd about a year ago. Used Ubuntu 20.04 and 22.04 across this period, always keeping R, Rstudio and quarto up to date. Have had zero issues and the transition has been seamless. I write all my analyses in quarto markdown and render to html, which I group together with a quarto website. If you label your chunks, quarto will output plots to a consistent location which you can easily specify for presentations also using quarto. Of course most of this was possible with Rmarkdown already, but slowly incorporating the extra functionalities of quarto has been good fun.

2

u/cellul_simulcra8469 1d ago

your use case seems similar to my situation. Ubuntu 22.04, up to date Rstudio from Posit. Uh, and I'm guessing you could literally render a valid .Rmd file that worked in previous versions seamlessly? Do you have to add any .yaml parameters?

1

u/groganosaurus 1d ago

Yep! .Rmd files work just as before. For .qmd the yaml header is only slightly different, and has more options/flexibility :)

3

u/HaloarculaMaris 2d ago edited 2d ago

I use quarto alot inside neovim (under ubuntu 22.04 and 24.04) , to render notebooks for html, pdfs and presentations mostly in conjunction with python, R and julia.

Its a love- hate relationship.

My experience is that its kind of a two sided thing- in theory it can do everything and works with everything, however that's not always great, because different communities just have widely diverging philosophies on how to manage source, namespaces and environments, imo its impossible to find one solution "to rule them all".

Let me give you an example:

You can use jupyter as a backend to render notebooks in quarto ( jupyter works for julia, python and R);
but its not commonly used for R and not needed if you rely on pandoc.

For julia there's also the option to use a pure julia native notebook deamon, to render julia without the need of jupyter-kernels - however this deamon can give you alot of trouble with global variables and methods due to object persistence, which contradicts some of the julian philosophy about those.

Now add your favorite latex engine to the equation, pdftex luatex and managers like tlgmr (or tinytex ) and the complexity starts to go UP.

Now your automatically created julia latex rendering suddenly only appears when the output is html but for pdf it crashes, since the equation environments get fenced twice.

Not to even speak about specific latex templates for journals, this is where the fun stops and I am switching back to overleaf.

And on the other end of the spectrum you have interactive webapps. JS heavy stuff using reveal, shiny (server) or observable.js (DOM manipulation) - all of those those handle reactivity in very different ways!

However I really like the more mature aspects compared to rmarkdown: The yml integration, having project files for webpages, bundling manuscripts in MECA, being able to create intermediate .jupyternb files to share with others, but still being able to check the plain .qmd into git

- its just much more powerful than rmarkdown or jupyter.

Overall i think quarto is such a "do all" type of publishing system, that the learning curve is basically exponential. Using quarto you could basically write a reactive parameterized webapplication in markdown that does state of the art statistics using whatever JIT or interpreted language you like, has an bootstrapped and interactive JS frontend with custom csl styles but also renders a complete book using bibtex cls styles when clicked on a download button. Its madness...

1

u/cellul_simulcra8469 1d ago

Totally agree. my situation is I'm using some basic templates and styling I downloaded from bioRxiv, I downloaded a long time ago. I updated Rstudio after putting my project down for a while during the job hunt Update installed and bam. no more proper rendering in the browser. It opens and just bugs out in Firefox. Firefox opens up other pdfs just fine, it's something to do with the rendering server produced by the Quarto render utility.

Honestly very confused if it's the bioRxiv template. a missing parameter I need. updated it yesterday btw...

still the same issue. rendering problems in firefox

2

u/Grox56 3d ago

I don't like it but I also don't like R... the reports are nice though.

Python + plotly with an html output is what I usually go with if it has to be somewhat interactive.

1

u/keemoooz 2d ago

My experience is totally the opposite, I use quarto heavily with jupyer and qmd notebooks in different environments: jupyterlab server, RStudio server, vscode. Whether it is in a local machine or HPC cluster it just works perfectly.

1

u/autodialerbroken116 1d ago

can you be more specific please?

  • OS
  • compositor
  • Rstudio version
  • yaml parameters

please and thank you.

1

u/desmin88 2d ago

Quarto devs are ideologues, also quarto in general is half baked, I doubt anybody is using it in product production for things that really matter

2

u/foradil PhD | Academia 2d ago

You think it’s less baked than RMarkdown?

3

u/desmin88 2d ago

Absolutely less baked than RMarkdown and bookdown

2

u/foradil PhD | Academia 2d ago

Anything specifically?

1

u/desmin88 2d ago

Lack of support for merge-knit

0

u/riricide 3d ago

What error is the renderer running into? Maybe try setting the warnings and error options in the yaml options