Project render fails with "Directory not empty (os error 39)" removing execute-results when the project is on NFS

Start in src/command/render/render-files.ts at renderExecute(), where removeFreezeResults() deletes the execute-results directory right after the freeze copy, and follow the call into safeRemoveSync(). The failure is an ENOTEMPTY race on NFS that cannot be reproduced on local disk, so first decide between a retry with backoff, a warning instead of a fatal error, or skipping the write when freeze is off. Done means a project render on NFS no longer aborts, with an existing test or a new one covering the removal path.

Bug description

Rendering a knitr document inside a Quarto project that lives on an NFS mount fails intermittently, after all code has executed and before pandoc runs:

processing file: analysis.qmd
output file: analysis.knit.md

ERROR: Directory not empty (os error 39): remove '/nfs/project/analyses/analysis_files/execute-results'

Stack trace:
    at Object.removeSync (ext:deno_fs/30_fs.js:250:3)
    at safeRemoveSync (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:3228:10)
    at removeIfExists (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:7970:5)
    at removeFreezeResults (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:136700:3)
    at renderExecute (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:136863:5)
    at async renderFileInternal (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:137094:35)
    at async renderFiles (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:136884:9)
    at async renderProject (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:137468:23)

Immediately afterwards, ls -la analysis_files/execute-results/ shows the directory is empty.

What seems to happen

In a project render, renderExecute() (src/command/render/render-files.ts) writes the freeze result <doc>_files/execute-results/html.json, copies it to the freezer, and then calls removeFreezeResults(), which removes execute-results right away (the project does not use freeze). On NFS, unlinking a file whose handle has not fully closed triggers the client's "silly rename": the file becomes a hidden .nfsXXXX placeholder until the last handle closes. The directory is therefore briefly non-empty, removeSync fails with ENOTEMPTY, and the render aborts. By the time a user inspects the directory, the placeholder is gone.

This fits the observations:

• It happens after all code has run, so every chunk's side effects (saved files, figures) exist, but no HTML is written.
• It is intermittent. The same document sometimes renders cleanly, and long documents with large output seem more affected.
• It never happens with the same files on local disk.
• It never happens outside a project (single-file renders take a different path that skips the freeze write).

Reproduction

1. A Quarto project (_quarto.yml with project: type: default) on an NFS-mounted directory.
2. A knitr .qmd with substantial printed output and a figure.
3. quarto render path/to/doc.qmd repeatedly; some runs fail as above.

We cannot share our documents (clinical data), and the failure depends on NFS timing, so a minimal example on local disk will not reproduce it.

Workaround

Make execute-results a symlink to a directory on local disk before rendering:

files_dir="doc_files"
local_dir="$(mktemp -d)"
rm -rf "$files_dir" && mkdir -p "$files_dir"
ln -s "$local_dir" "$files_dir/execute-results"
quarto render doc.qmd

Quarto writes html.json through the link and, on cleanup, removes the link itself, so nothing is unlinked on NFS. The render then succeeds, with project mode and pre/post-render scripts intact. (Symlinking the whole _files directory instead does not work: the final cleanup refuses to remove a directory that resolves outside the project.)

Possible fixes

• Retry the removal of execute-results on ENOTEMPTY/EBUSY with a short backoff, as many tools do for NFS.
• Treat failure to remove execute-results as a warning rather than a fatal error, since the freeze result has already been copied to the freezer.
• When freeze is not enabled, skip writing execute-results/html.json beside the document at all.

Environment

• Quarto 1.10.18 (bundled with Posit Workbench)
• R 4.6.1, knitr 1.51, rmarkdown 2.31
• RHEL 8.10, project directory on an NFS mount

Related

#2380 also concerns projects on network storage, but it is a Windows UNC path-resolution failure (os error 3); this is a Linux NFS delete race (os error 39).