Summary

prek install-hooks for node-language hooks (e.g. prettier, markdownlint-cli2) reports success but the hook env's bin/ and lib/node_modules/ stay empty. Running the hook then fails with:

error: Failed to run hook `prettier`
  caused by: Run command `node hook` failed
  caused by: No such file or directory (os error 2)

Root cause

prek's npm invocation sets the uppercase NPM_CONFIG_PREFIX env var but does not strip the lowercase npm_config_prefix / npm_config_global_prefix / npm_config_local_prefix / npm_config_globalconfig from the inherited environment. POSIX env vars are case-sensitive, so both reach npm as distinct keys; npm normalizes them to lowercase during config parsing, and the inherited lowercase entries win over prek's uppercase override.

The result: npm install -g <pkg> installs into whatever the parent shell's npm_config_prefix points at, not into prek's hook env. The npm process exits 0, prek writes .prek-hook.json based only on that exit code, and the next run fails because bin/ is empty. The marker file then makes the failure sticky — subsequent prek runs short-circuit on "already installed" and reproduce the same error even after the polluting env is unset.

npm exec / npx propagate these lowercase vars automatically to child processes, so anything that runs prek as a descendant of an npx/npm invocation reproduces the bug.

Minimal reproduction

mkdir /tmp/prek-repro && cd /tmp/prek-repro
git init -q

cat > prek.toml <<'EOF'
[[repos]]
repo = "https://github.com/rbubley/mirrors-prettier"
rev = "v3.8.3"
hooks = [{ id = "prettier" }]
EOF
echo '{"a":1}' > test.json
git add -A

# Simulate an inherited polluted env (this is what `npx` does to its children):
export npm_config_prefix=/tmp/fake-prefix
export npm_config_global_prefix=/tmp/fake-prefix
export npm_config_local_prefix=/tmp/fake-prefix
mkdir -p /tmp/fake-prefix

prek clean
prek install-hooks                                # reports success

ls ~/.cache/prek/hooks/node-*/bin/                # empty
ls /tmp/fake-prefix/lib/node_modules/             # prettier installed here

prek run prettier --files test.json
# error: Failed to run hook `prettier`
#   caused by: Run command `node hook` failed
#   caused by: No such file or directory (os error 2)

Workaround

env -u npm_config_prefix -u npm_config_globalconfig \
    -u npm_config_local_prefix -u npm_config_global_prefix \
    -u npm_config_cache -u npm_config_userconfig \
    prek install-hooks

If already bitten, also prek clean (or rm -rf ~/.cache/prek/hooks/node-*) to drop stale .prek-hook.json markers.

Proposed fix

In both the install and run impls in crates/prek/src/languages/node/node.rs, additionally .env_remove() the lowercase npm config env vars before invoking npm / the hook entry. Minimum set:

• npm_config_prefix
• npm_config_global_prefix
• npm_config_local_prefix
• npm_config_globalconfig
• npm_config_cache
• npm_config_userconfig

A more robust version would scrub every npm_config_* (lowercase) key from the child env — they're an implementation detail of npm exec propagating its config to child scripts, and nothing inside the hook env needs them.

Defensive secondary fix: after npm install returns success, verify env_path/bin/ is non-empty before writing .prek-hook.json. That would surface this class of bug as an install-time error rather than a silent success + cryptic run-time failure.

Willing to submit a PR?

• Yes — I'm willing to open a PR to fix this.

Platform

Darwin 25.4.0 arm64

Version

prek 0.3.13 (Homebrew 2026-05-05)

.pre-commit-config.yaml

(Using prek.toml, not .pre-commit-config.yaml. Minimal config that reproduces:)

[[repos]]
repo = "https://github.com/rbubley/mirrors-prettier"
rev = "v3.8.3"
hooks = [{ id = "prettier" }]

Log file

2026-05-11T17:43:58.909701Z TRACE Executing `/Users/me/.asdf/installs/nodejs/24.13.0/bin/npm install -g --no-progress --no-save --no-fund --no-audit --install-links /Users/me/.cache/prek/repos/80d0aae29b041cec [...]`
2026-05-11T17:43:58.948719Z TRACE Executing `/Users/me/.asdf/installs/nodejs/24.13.0/bin/npm install -g --no-progress --no-save --no-fund --no-audit --install-links /Users/me/.cache/prek/repos/965e662e79e8d127 [...]`
2026-05-11T17:43:59.475736Z DEBUG Installed hook `prettier` in `/Users/me/.cache/prek/hooks/node-XiROg2uNqnXGKGfMB2yX`
2026-05-11T17:44:00.742826Z DEBUG Installed hook `markdownlint-cli2` in `/Users/me/.cache/prek/hooks/node-jLuibkjB0k983KoDePA0`

# ...subsequent `prek run prettier`:
2026-05-11T17:44:00.804224Z DEBUG Found installed environment for hook `prettier` at `/Users/me/.cache/prek/hooks/node-XiROg2uNqnXGKGfMB2yX`
2026-05-11T17:44:00.816487Z TRACE run{hook_id=prettier language=node}: Resolved command: prettier
2026-05-11T17:44:00.816562Z TRACE run{hook_id=prettier language=node}: Executing `cd /Users/me/agent_harness && prettier --write --ignore-unknown <file>`
2026-05-11T17:44:00.818638Z TRACE run{hook_id=prettier language=node}: close time.busy=2.40ms time.idle=30.7µs
error: Failed to run hook `prettier`
  caused by: Run command `node hook` failed
  caused by: No such file or directory (os error 2)

The "Installed hook" messages above are emitted on npm-exit-0 regardless of whether env_path/bin/ was actually populated; inspecting that directory shows it is empty, while <value of $npm_config_prefix>/lib/node_modules/ contains the package that should have gone into the hook env.