Why is my embeded HTML file deleted and replaced by an old version when I refresh my browser page?

[ronblum]

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

[Filed originally by @fredericvergnaud at https://github.com/rstudio/rstudio/issues/16854]

System details

RStudio Edition : Desktop
RStudio Version : 2026.01.0+392
OS Version      : MacOS Tahoe 26.2
R Version       : 4.5.1

Quarto is behaving strangely with my bibliography.
I want to incorporate a bibliography into my website generated by Quarto.
Since I only want the final result, an HTML file bibliography.html that I want to insert with an iframe into a qmd file, I proceed as follows (a video would be needed to describe the problem properly, but I will try to be precise):

• I have a bibliography linked to Zotero: this works very well
• I integrate references into a references.qmd file: this works very well, the references.bib file is created correctly
• I run a render of references.qmd to generate a references.html file in the public directory: this works very well
• Since I only want to keep this HTML file, I move it to the root directory and rename it bibliography.html: OK
• I create a new bibliography.qmd file in which I write the code to insert an iframe:

<iframe src="./bibliography.html"></iframe>

• At this point, my bibliography.html file is correct: I can modify it and remove the references to keep only the bibliography itself
• It is when I run the render of bibliography.qmd, which only contains the iframe call from bibliography.html, that my bibliography.html file is deleted and no longer contains my bibliography. Instead, I get:
• My website structure: header, menu, footer
• In the body: only JavaScript: an event listener, then the following functions: onCopySuccess, getTextToCopy, a test on quarto-embedded-source-code-modal, tippyHover, processXRef ... and at the end a bibliorefs variable that seems related to what I want, but which doesn't display anything.

Do you understand any of this? And if so, what do I need to do to simply insert my bibliography.html file via bibliography.qmd without it being destroyed by subsequent quarto render commands?

• [ x] I have read the guide for submitting good bug reports.
• [ x] I have installed the latest version of RStudio, and confirmed that the issue still persists.
• If I am reporting an RStudio crash, I have included a diagnostics report.
• [ x] I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.

Steps to reproduce

No response

Actual behavior

No response

Expected behavior

No response

Your environment

No response

Quarto check output

Not sure--it's not in the original bug report. However, I reproduced it with Quarto 1.8.27.

$ quarto check
Quarto 1.8.27
[>] Checking environment information...
      Quarto cache location: C:\Users\RonBlum\AppData\Local\quarto
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.3.1: OK
      Typst version 0.13.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.8.27
      Path: C:\Program Files\Quarto\bin
      CodePage: 1252

[>] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[>] Checking LaTeX....................OK
      Using: TinyTex
      Path: C:\Users\RonBlum\AppData\Roaming\TinyTeX\bin\windows\
      Version: 2025

[>] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: C:\Program Files\Google\Chrome\Application\chrome.exe
      Source: Windows Registry

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....OK
      Version: 3.13.6
      Path: C:/Users/RonBlum/AppData/Local/Programs/Python/Python313/python.
exe
      Jupyter: 5.8.1
      Kernels: python3

[>] Checking Jupyter engine render....OK

(\) Checking R installation............Rprofile ...
(|) Checking R installation............Rprofile ... done
[>] Checking R installation...........OK
      Version: 4.5.2
      Path: C:/PROGRA~1/R/R-45~1.2
      LibPaths:
        - C:/Users/RonBlum/AppData/Local/R/win-library/4.5
        - C:/Program Files/R/R-4.5.2/library
      knitr: 1.51
      rmarkdown: 2.30

[>] Checking Knitr engine render......OK

[mcanouil]

Do you have an actual concrete reproducible example, preferably small?

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code block (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[fredericvergnaud]

Hi,

I have originally created a repo here to reproduce the scenario : https://github.com/fredericvergnaud/test-embedded-HTML-file

One way to reproduce the problem :

• remove bibliography.html from public
• copy references.html at the root, rename it to bibliography.html and make some modifications
• run quarto render

Outputs :

• the file bibliography.qmd that call bibliography.html in an iframe doesn't work
• the file bibliography.html in public has been erased by the render

My working solution is to directly add a bibliography.html file in public, but this solution is not viable at middle or long term.

Thanks for your help !

[mcanouil]

A quick look at your repository shows a infinite recursive inclusion which is obviously not going to end/work well:

• bibliography.qmd will be rendered by Quarto as bibliography.html.
• bibliography.qmd has an iframe including bibliography.html, thus it includes itself.

What do you expect to do here? What's the issue you are trying to address with this?

To me there are no bugs, only unexpected project setup.

[fredericvergnaud]

I'm sorry, I've made changes to my files, as suggested by @ronblum here :

• renamed bibliography.qmd to bibliography_wrapper.qmd
• updated the _quarto.yml navbar to refer to bibliography_wrapper.qmd

When i did this 2 days ago, it doesn't worked, but I just retested it, and it works perfectly. Surely I did it the wrong way. Sorry for the inconvenience.

[mcanouil]

it doesn't worked, but I just retested it, and it works perfectly.

I don't know what this means, but seems there is no longer an issue.

Be aware that, upon render, Quarto will erase everything in output-dir unless told otherwise from the CLI (see --no-clean).
In some cases, resources not directly used by Quarto can be missed, in those cases, you want to be explicit about them and list them under project.resources (https://quarto.org/docs/websites/website-tools.html#site-resources)

For the future, if you have questions about Quarto behaviours, please open a Q&A discussion after looking through issues and discussions: https://github.com/orgs/quarto-dev/discussions

[fredericvergnaud]

Thank you @mcanouil
I didn't moved the topic to bug, @ronblum did it. I have originally posted my message in RStudio issues

[mcanouil]

I didn't moved the topic to bug, @ronblum did it. I have originally posted my message in rstudio/rstudio#16854

I know, I'm only telling you where you might find answers and where to ask questions if new ones come up in the future. Nothing more.

[fredericvergnaud]

Ok, thanks