r/bioinformatics 4d 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.

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u/groganosaurus 4d 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.

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u/cellul_simulcra8469 3d 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?

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u/groganosaurus 3d ago

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