Cannot produce html_notebook output with R-rmarkdown

Ask Fedora
1

Hello Fedora community,

I have troubles rendering a Rmarkdown html_notebook in Fedora 39.

On Ubuntu (toolbox) it works fine just installing rmarkdown and texlive, but in Fedora it complains of missing

/usr/share/R/library/rmarkdown/rmd/h/bootstrap/css/../fonts/glyphicons-halflings-regular.eot

Querying for dnf provides */fonts/glyphicons-halflings-regular.eot gave some results, but also install R-bslib, R-shiny, python3-XStatic-Bootstrap-SCSS and python3-sphinx-bootstrap-theme did not work.

Full error message is as follows

Rscript -e "rmarkdown::render('test.rmd')"


processing file: test.rmd

output file: test.knit.md

/usr/bin/pandoc +RTS -K512m -RTS test.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output test.html --lua-filter /usr/share/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/share/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/share/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpGGcGgv/rmarkdown-strbff07178b59f.html --variable code_folding=show --variable source_embed=test.rmd --include-after-body /tmp/RtmpGGcGgv/filebff01dfc2ece.html --variable code_menu=1 --variable kable-scroll=1
pandoc: /usr/share/R/library/rmarkdown/rmd/h/bootstrap/css/../fonts/glyphicons-halflings-regular.eot: withBinaryFile: does not exist (No such file or directory)
Errore: pandoc document conversion failed with error 1

and this is test.rmd file

---
title: "A test"
output:
    html_notebook
---

This is a test for an `.rmd` file.

Am I missing something to install?

2

It requires that you work through the errors one at a time and install the missing file each time until you are successful. This may occur any time you install a 3rd party package that is “out of tree” in the repos. Installing from the fedora and compatible repos usually pulls in the required dependencies, but when out of tree you are required to solve those issues as they are seen.

I don’t know about the html_notebook tool. On my system, using dnf to installR-rmarkdown would pull in 229 different packages, the majority of which are R-* or texlive-* or perl-*. Did you install R-rmarkdown with dnf?

3

Yes, I did. I installed with dnf all above mentioned packages.

Moreover, it complains of missing glyphicons-halflings-fontsbut I have it installed.

4

Are you in Fedora 39 (Host) using toolbox with a minimal Fedora image?

5

Yes, F39 host, toolbox F39 with R-rmarkdown, texlive full and pandoc installed.

6

The R-rmarkdown package includes /usr/share/R/library/rmarkdown/rmd/h/bootstrap/fonts/glyphicons-halflings-regular.ttf, but not .eot

I’d guess this is a bug in that package. It strips all the bundled fonts out and replaces them with symlinks to system fonts, but glyphicons-halflings-fonts only includes the .ttf.

https://src.fedoraproject.org/rpms/R-rmarkdown/blob/rawhide/f/R-rmarkdown.spec#_217

    pushd rmd/h/bootstrap/fonts
        rm -f glyphicons-halflings*
        ln -sf /usr/share/fonts/glyphicons-halflings/glyphicons-halflings-regular.ttf glyphicons-halflings-regular.ttf
    popd

I don’t know if it’s expected to work without the .eot. Please file a bug against R-rmarkdown.

7

Alright, I’ll do in in some hours. Thank you for the support

8

The omission of eot fonts from Fedora packages is deliberate. See Fonts :: Fedora Docs.

9

@jjames Thanks for inadvertantly pointing me to the Docs i was looking for this afternoon !

10

Okay, so it’s upstream’s problem. I will use my custom CSS as a good workaround for that

Thank you very much

11

I do think a bug report is still warranted. This could be addressed upstream, but it’s ultimately only broken because of a downstream change made to comply with Fedora policy.