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--output-dir warns about non-empty directories, but deletes contents anyway #13623

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--output-dir warns about non-empty directories, but deletes contents anyway#13623
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cderv
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v1.12

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@eheinzen
eheinzen
opened on Oct 28, 2025

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

I'm running quarto 1.8.24. When I specify --output-dir, it first warns about it not being an empty directory, but deletes files therein anyway:

Steps to reproduce

$ mkdir test_quarto
$ cd test_quarto
$ echo '---
> title: "Untitled"
> format: html
> ---' > test.qmd
$ mkdir important_files
$ echo 'Something important!' > important_files/do_not_delete.txt
$ quarto render test.qmd --output-dir important_files
ERROR: Directory not empty (os error 39): remove '<sensitive path>/test_quarto/.quarto'

Stack trace: <...>

$ cat important_files/do_not_delete.txt # It's not there!
cat: important_files/do_not_delete.txt: No such file or directory

However, it doesn't have this behavior with a _quarto.yml

$ mkdir test_quarto
$ cd test_quarto
$ echo '---
> title: "Untitled"
> format: html
> ---' > test.qmd
$ echo 'project:
>   output-dir: important_files' > _quarto.yml
$ mkdir important_files
$ echo 'Something important!' > important_files/do_not_delete.txt
$ quarto render test.qmd
  
Output created: important_files/test.html

$ cat important_files/do_not_delete.txt # It's there!
Something important!

Actual behavior

Deletes my files.

Expected behavior

Don't delete my files.

Your environment

Linux

Activity

  1. eheinzen
    added
    bugSomething isn't working
    on Oct 28, 2025

  2. mcanouil commented on Oct 28, 2025

    @mcanouil
    mcanouil
    on Oct 28, 2025
    Collaborator

    @eheinzen Could you format your code for it to be usable? Thank you.

    Also please provide the output of quarto check as requested in the template.

    Note that the behaviour in project is to delete all the output directory (if/when inside the project). Have you consider looking at the help of the CLI? quarto render --help, especially the --no-clean flag?

  3. mcanouil
    added
    needs-reproIssues that are blocked until reporter provides an adequate reproduction
    on Oct 28, 2025

  4. eheinzen commented on Oct 28, 2025

    @eheinzen
    eheinzen
    on Oct 28, 2025
    Author

    Sorry, was trying to incorporate the output at the same time as the code, which I now realize makes your job harder!

    mkdir test_quarto
cd test_quarto
echo '---
title: "Untitled"
format: html
---' > test.qmd
mkdir important_files
echo 'Something important!' > important_files/do_not_delete.txt
quarto render test.qmd --output-dir important_files
cat important_files/do_not_delete.txt # It's not there!

    quarto check has a lot of sensitive paths in it that I needed to scrub out:

    $ quarto check
Quarto 1.8.24
[✓] Checking environment information...
      Quarto cache location: /home/.../.cache/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: 1.8.24
      Path: /.../software/quarto/quarto-1.8.24/bin

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

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/.../.TinyTeX/bin/x86_64-linux
      Version: 2023

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /usr/bin/chromium-browser
      Source: PATH

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

[✓] Checking Python 3 installation....OK
      Version: 3.6.8
      Path: /usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 4.2.2
      Path: /.../software/R/R-4.2.2/lib64/R
      LibPaths:
        - /.../renv/library/R-4.2/x86_64-pc-linux-gnu
        - /.../software/R/R-4.2.2/lib64/R/library
      knitr: 1.45
      rmarkdown: 2.25

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

    I'll take a look at that other documentation. Wasn't aware of that option; I was just surprised when all my files in my output directory got deleted.

  5. eheinzen commented on Oct 28, 2025

    @eheinzen
    eheinzen
    on Oct 28, 2025
    Author

    Update: --no-clean retains the files in the output directory, which is what I want. Should that be the default behavior? It behaves that way when you use the _quarto.yml (that is: no files get deleted).

  6. mcanouil commented on Oct 28, 2025

    @mcanouil
    mcanouil
    on Oct 28, 2025
    Collaborator

    It behaves that way when you use the _quarto.yml (that is: no files get deleted).

    That's not true. As I said, all files get deleted when output directory is within the project which is the expected location (at least for all non "default" projec type). Content is not deleted when it's outside of the project because there are risks to delete something not at all tied to the project.

    "single documents" are also a "project" which for now does not behave exactly the same way as "default" project.

  7. mcanouil
    removed
    needs-reproIssues that are blocked until reporter provides an adequate reproduction
    on Oct 28, 2025

  8. mcanouil commented on Oct 28, 2025

    @mcanouil
    mcanouil
    on Oct 28, 2025
    Collaborator

    Also, here you are using project.output-dir and --output-dir which are known to not behave exactly the same way as discussed in:

    See a pretty much comprehensive overview of the behaviours in the comment: #2171 (comment)

    Output directory cleaning seems to be another discrepancy between "default", "single document" projects, and the other types of project.

    Anyhow, because some users might already rely on the current behaviour, a change in the default is unlikely to happen at the moment as it could lead to a lot of breakage. The --no-clean flag is there precisely to avoid cleaning.

  9. mcanouil
    added
    projects
    on Oct 28, 2025

  10. eheinzen commented on Oct 28, 2025

    @eheinzen
    eheinzen
    on Oct 28, 2025
    Author

    Thanks for the explanation! That makes more sense now.

    Output directory cleaning seems to be another discrepancy between "default", "single document" projects, and the other types of project.

    This is where I was getting stuck. To me, deleting all files in an output directory doesn't ever seem like a good idea, and I was getting hung up on it working in some places but not others. For now, I'll stick with --no-clean.

  11. mcanouil commented on Oct 28, 2025

    @mcanouil
    mcanouil
    on Oct 28, 2025
    Collaborator

    In most projects, you don't want outdated files to stick thus the cleaning default.

  12. cderv commented on Oct 29, 2025

    @cderv
    cderv
    on Oct 29, 2025
    Member

    It is an interesting use case because it reliably recreate on windows the OSERROR 32

    ERROR: Le processus ne peut pas accéder au fichier car ce fichier est utilisé par un autre processus. (os error 32): remove 'C:\Users\chris\AppData\Local\Temp\quarto\test_quarto\.quarto'

    I'll have a look in this.

  13. cderv
    self-assigned this
    on Oct 29, 2025

  14. mcanouil commented on Oct 29, 2025

    @mcanouil
    mcanouil
    on Oct 29, 2025
    Collaborator

    I realised I forgot to mention that the error is indeed limited to Windows.

  15. cscheid
    added this to the Future milestone on Feb 13, 2026

  16. cderv commented on Jun 30, 2026

    @cderv
    cderv
    on Jun 30, 2026
    Member

    Looking at this again, there are two separate issues here.

    I believe the error on .quarto removal (Directory not empty on Linux, os error 32 on Windows) was fixed in #13626 — the cleanup was doing things in the wrong order, attempting to remove the .quarto scratch directory before closing the Deno KV file handle inside it. That's been resolved since v1.9.

    The data loss part — pre-existing files in the output directory being deleted — is still present. I can reproduce it on current main. The root cause is that --output-dir without a _quarto.yml creates a synthetic project context and sets a forceClean flag, which incorrectly triggers output directory cleaning regardless of project type. With a _quarto.yml that sets project.output-dir, the synthetic path is never taken, so files are preserved — which explains the difference you observed.

    The fix could be straightforward: the forceClean flag conflates two things (cleaning the output directory, and cleaning up the temporary .quarto scratch directory). Only the latter should apply for single-file renders. I'll track a fix.

  17. cderv
    modified the milestones: Future, v1.10 on Jun 30, 2026
  18. cderv
    added 2 commits that reference this issue on Jun 30, 2026

    fix: don't clean output dir for single-file --output-dir renders (#13623

    ae88444

    fix: don't clean output dir for single-file --output-dir renders (#13623

    fa2acb5
  19. mcanouil
    modified the milestones: v1.10, v1.11 on Jul 30, 2026
  20. cderv
    modified the milestones: v1.11, v1.12 on Oct 29, 2026
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