Fix quarto preview crash on knitr document in a project subdirectory

.claude/rules/testing/test-anti-patterns.md

@@ -17,3 +17,9 @@ paths:
 Never create `Project.toml`, `.venv/`, or `renv.lock` in test fixture directories.
 
 **Details:** `llm-docs/testing-patterns.md` → "Shared Test Environments"
+
+## Don't: `Deno.chdir()` inside the test body
+
+`Deno.chdir()` mutates process-global cwd, so a test that changes it can leak into other tests in the same process. The harness already changes and restores the working directory: return the directory from `TestContext.cwd`, create fixtures in `setup`, clean up in `teardown` (examples: `tests/unit/dotenv-config.test.ts`, `tests/smoke/use/template.test.ts`). For a temp directory you don't need to run *from*, use `withTempDir` (`tests/utils.ts`). A test that only needs a *relative* input can pass a path relative to the current cwd without changing it.
+
+**Details:** `llm-docs/testing-patterns.md` → "Working-Directory-Sensitive Tests"

.claude/rules/testing/unit-test-with-r.md

@@ -0,0 +1,15 @@
+---
+paths:
+  - "tests/unit/preview-subdir-knitr-cwd.test.ts"
+---
+
+# R unit test that changes working directory
+
+This test runs a knitr subprocess with cwd set to a scratch directory
+(required to reproduce the bug). R's `.Rprofile` lookup is cwd-exact, so it
+won't pick up `tests/renv` activation there — on CI the R subprocess fails
+with `there is no package called 'rmarkdown'`. `setup()` writes a
+`.Rprofile` into the fixture dir to re-activate renv against the real
+`tests/` project.
+
+**Details:** `llm-docs/testing-patterns.md` → "R Tests That Change Working Directory"

llm-docs/testing-patterns.md

@@ -169,6 +169,40 @@ testQuartoCmd(
 - Clean up entire temp directory including source files
 - File verification uses relative paths when checking files in `cwd()`
 
+### Working-Directory-Sensitive Tests
+
+Some tests need to run from a specific directory (e.g. reproducing a bug that
+depends on the process cwd). **Do not `Deno.chdir()` inside the test body** —
+it mutates process-global cwd and can leak into other tests in the same
+process. Use the `TestContext` options instead; the harness changes the cwd
+before the test and restores it afterward:
+
+```typescript
+const workingDir = Deno.makeTempDirSync();
+
+unitTest("runs from workingDir", async () => {
+  // cwd is workingDir here (set by the harness)
+}, {
+  setup: () => { Deno.writeTextFileSync(".env.example", "..."); return Promise.resolve(); },
+  cwd: () => workingDir,
+  teardown: () => { try { Deno.removeSync(workingDir, { recursive: true }); } catch { /* best-effort */ } return Promise.resolve(); },
+});
+```
+
+**Key points:**
+
+- The harness calls `cwd()` **before** `setup()`, so the directory must already
+  exist when `cwd()` runs — create it at module scope, not in `setup`.
+- `teardown` runs **before** the harness restores the cwd, so on Windows the
+  temp dir may still be the cwd and resist removal. Wrap the removal in
+  try/catch (best-effort) — see `tests/smoke/use/template.test.ts` and
+  `tests/unit/dotenv-config.test.ts`.
+- For a temp directory you don't need to run *from*, prefer `withTempDir`
+  (`tests/utils.ts`), which creates and recursively removes it in a `finally`.
+- A test that only needs a **relative** input (not a specific cwd) can pass a
+  path relative to the current cwd (`relative(Deno.cwd(), absFile)`) without
+  changing directories at all.
+
 ## Verification Helpers
 
 ### Core Verifiers
@@ -363,6 +397,36 @@ Rscript -e "renv::install(); renv::snapshot()"
 
 **Note:** While Quarto supports local Project.toml files in document directories for production use, the quarto-cli test infrastructure specifically does NOT support this pattern. All test dependencies must be in the main `tests/` environment.
 
+### R Tests That Change Working Directory
+
+R resolves `.Rprofile` from the **exact** process cwd (no parent-directory
+search). On CI, rmarkdown/knitr live only in `tests/renv`'s project library,
+activated when cwd is `tests/` (via `tests/.Rprofile` sourcing
+`renv/activate.R`). Most knitr tests never leave `tests/` — they pass paths
+relative to the current cwd instead of changing directories — so activation
+happens automatically.
+
+A test that must run with cwd set elsewhere (a scratch temp dir, via
+`TestContext.cwd()` — see "Working-Directory-Sensitive Tests" above) loses
+that activation: the R subprocess starts outside `tests/`, renv never
+activates, and package loads fail with `there is no package called
+'rmarkdown'`. This is CI-only — a developer machine with rmarkdown on the
+default `.libPaths()` masks it entirely. The render pipeline also tends to
+swallow the underlying subprocess error, so the failure can be silent beyond
+the bare package-load message.
+
+**Fix:** in the fixture's cwd, write a `.Rprofile` that re-points renv at the
+real project, regardless of where the test's cwd actually is:
+
+```r
+Sys.setenv(RENV_PROJECT = "<absolute path to tests/>")
+source("<absolute path to tests/>/renv/activate.R")
+```
+
+`renv/activate.R` reads `RENV_PROJECT` to determine the project root if set,
+falling back to `getwd()` otherwise — setting it explicitly decouples renv
+activation from the test's cwd.
+
 ## Best Practices
 
 1. **Always clean up**: Use teardown to remove generated files

news/changelog-1.10.md

@@ -6,6 +6,7 @@ All changes included in 1.10:
 - ([#14281](https://github.com/quarto-dev/quarto-cli/issues/14281)): Fix transient `.quarto_ipynb` files accumulating during `quarto preview` with Jupyter engine.
 - ([#14298](https://github.com/quarto-dev/quarto-cli/issues/14298)): Fix `quarto preview` browse URL including output filename (e.g., `hello.html`) for single-file documents, breaking Posit Workbench proxied server access.
 - ([#14489](https://github.com/quarto-dev/quarto-cli/issues/14489)): Restore `--output-dir` support for `quarto preview` of single files when no `_quarto.yml` is present (e.g. R-package workspaces). Regression introduced in v1.9.18.
+- ([#14683](https://github.com/quarto-dev/quarto-cli/issues/14683)): Fix `quarto preview` of a knitr document in a project subdirectory failing when run from that subdirectory with a bare filename (the shape RStudio's Render button uses). Regression introduced in v1.9.18.
 - ([rstudio/rstudio#17333](https://github.com/rstudio/rstudio/issues/17333)): Fix `quarto inspect` on standalone files emitting project metadata that breaks RStudio's publishing wizard.
 
 ## Dependencies
@@ -108,6 +109,7 @@ All changes included in 1.10:
 - ([#6092](https://github.com/quarto-dev/quarto-cli/issues/6092)): Fix the `default-image-extension` being appended to an extensionless URL ending in a slash (e.g. `![](https://example.com/)`), which broke the embed/iframe image syntax.
 - ([#6651](https://github.com/quarto-dev/quarto-cli/issues/6651)): Fix dart-sass compilation failing in enterprise environments where `.bat` files are blocked by group policy.
 - ([#11703](https://github.com/quarto-dev/quarto-cli/issues/11703)): Fix SCSS color-variable export (`--quarto-scss-export-*`) being silently skipped when a theme rule contains consecutive semicolons (e.g. `max-height: 100% !important;;`).
+- ([#12401](https://github.com/quarto-dev/quarto-cli/issues/12401)): Fix `QUARTO_DOCUMENT_PATH` being a relative path for single-file renders, inconsistent with project renders where it was absolute. Execution target paths are now normalized to absolute at a single point, so single-file and project renders behave the same.
 - ([#14255](https://github.com/quarto-dev/quarto-cli/issues/14255)): Fix shortcodes inside inline and display math expressions not being resolved.
 - ([#14342](https://github.com/quarto-dev/quarto-cli/issues/14342)): Work around TOCTOU race in Deno's `expandGlobSync` that can cause unexpected exceptions to be raised while traversing directories during project initialization.
 - ([#14445](https://github.com/quarto-dev/quarto-cli/issues/14445)): Fix intermittent `Uncaught (in promise) TypeError: Writable stream is closed or errored.` aborting renders on Linux. `execProcess` now awaits and swallows the rejection from `process.stdin.close()` when the child closes its stdin first. The captured stderr is now also surfaced when `typst-gather analyze` falls back to staging all packages, so failures are diagnosable without bypassing `quarto`.

src/execute/engine.ts

@@ -12,7 +12,7 @@ import {
   partitionYamlFrontMatter,
   readYamlFromMarkdown,
 } from "../core/yaml.ts";
-import { dirAndStem } from "../core/path.ts";
+import { dirAndStem, normalizePath } from "../core/path.ts";
 
 import { metadataAsFormat } from "../config/metadata.ts";
 import { kBaseFormat, kEngine } from "../config/constants.ts";
@@ -355,6 +355,19 @@ export async function fileExecutionEngineAndTarget(
   flags: RenderFlags | undefined,
   project: ProjectContext,
 ): Promise<{ engine: ExecutionEngineInstance; target: ExecutionTarget }> {
+  // Establish an "always absolute" contract for the file path at this single
+  // convergence point for all callers (preview format-resolution, render, and
+  // project render). fileInformationCache keys are normalized to absolute
+  // (FileInformationCacheMap), so a caller passing a cwd-relative path — e.g.
+  // preview seeding the cache with the bare filename RStudio's Render button
+  // uses from a subdirectory — would otherwise store a target whose
+  // source/input stay relative under an absolute key, a stale value that a
+  // later absolute-path lookup reuses. Normalizing here keeps target.source and
+  // target.input consistent with the key and with project renders (which
+  // already pass absolute paths). See #14151 (the contract), #12401
+  // (QUARTO_DOCUMENT_PATH / cwd inconsistency), #14150 (doubled subdirectory),
+  // and #14683 (knitr abs_path failure previewing from a subdirectory).
+  file = normalizePath(file);
   const cached = ensureFileInformationCache(project, file);
   if (cached && cached.engine && cached.target) {
     return { engine: cached.engine, target: cached.target };

tests/docs/manual/preview/README.md

@@ -161,6 +161,13 @@ After every change to preview URL or handler logic, verify that single-file prev
 - **Expected:** HTTP 200. Browse URL may include path for non-index files in project context.
 - **Catches:** `isSingleFile` guard accidentally excluding real project files from path computation
 
+#### T33: knitr doc in a subdirectory — preview from that subdirectory (#14683)
+
+- **Setup:** Fixture `knitr-subdir-14683/` — a website project with a knitr doc at `labs/doc.qmd` (an `{r}` chunk plus a `QUARTO_DOCUMENT_PATH` echo). Requires R + `rmarkdown`/`knitr`.
+- **Steps:** From `knitr-subdir-14683/labs/` (the doc's own directory), run `quarto preview doc.qmd --to html --no-watch-inputs --no-browser --port XXXX` — the shape RStudio's Render button uses (bare filename, cwd = the doc's subdirectory).
+- **Expected:** Renders without `Error in rmarkdown:::abs_path(input)`; `_site/labs/doc.html` is produced showing `[1] 2` (the R chunk executed). The echoed `QUARTO_DOCUMENT_PATH` is the doc's absolute subdirectory (ends in `labs`), not `.` / the project root (#12401).
+- **Catches:** `fileExecutionEngineAndTarget` not normalizing the input to absolute — a cwd-relative `target.input`/`source` in the shared preview cache makes the knitr R subprocess (cwd = project dir) fail `abs_path` on the subdirectory-relative filename.
+
 ## Test Matrix: Format Change Detection (#14533)
 
 After every change to `previewRenderRequestIsCompatible` or the

tests/docs/manual/preview/knitr-subdir-14683/.gitignore

@@ -0,0 +1,4 @@
+/.quarto/
+/_site/
+**/*_files/
+**/*.quarto_ipynb

tests/docs/manual/preview/knitr-subdir-14683/_quarto.yml

@@ -0,0 +1,5 @@
+project:
+  type: website
+
+website:
+  title: "Knitr Subdir Preview (#14683)"

tests/docs/manual/preview/knitr-subdir-14683/index.qmd

@@ -0,0 +1,6 @@
+---
+title: Home
+---
+
+Home page. The regression fixture is `labs/doc.qmd` — preview it from the
+`labs/` directory with a bare filename (see T33).

tests/docs/manual/preview/knitr-subdir-14683/labs/doc.qmd

@@ -0,0 +1,20 @@
+---
+title: Claude Test
+engine: knitr
+---
+
+A knitr document in a project subdirectory. Previewing it from this `labs/`
+directory with a bare filename (`quarto preview doc.qmd`) is the shape
+RStudio's Render button uses, and is what regressed in #14683.
+
+```{r}
+1 + 1
+```
+
+The rendered output must show `[1] 2` above (the R engine executed), and
+`QUARTO_DOCUMENT_PATH` below must be this file's absolute directory (ending in
+`labs`), not `.` or the project root (#12401).
+
+```{r}
+cat("QUARTO_DOCUMENT_PATH:", Sys.getenv("QUARTO_DOCUMENT_PATH"))
+```