Cannot npm clean-install or npm install with generated pruned package-lock.json file

[dkindt]

Summary

Cannot npm clean-install or npm install with generated pruned package-lock.json file. Here's the output I get:

dan@mbp ~/p/n/p/json> npm i
npm error Cannot read properties of undefined (reading 'extraneous')
npm error A complete log of this run can be found in: /Users/myuser/.npm/_logs/2025-03-25T23_59_06_490Z-debug-0.log```

or 

```bash
dan@mbp ~/p/n/p/json [1]> npm ci
npm error code EUSAGE
npm error
npm error The `npm ci` command can only install with an existing package-lock.json or
npm error npm-shrinkwrap.json with lockfileVersion >= 1. Run an install with npm@5 or
npm error later to generate a package-lock.json file, then try again.
npm error
npm error Clean install a project
npm error
npm error Usage:
npm error npm ci
npm error
npm error Options:
npm error [--install-strategy <hoisted|nested|shallow|linked>] [--legacy-bundling]
npm error [--global-style] [--omit <dev|optional|peer> [--omit <dev|optional|peer> ...]]
npm error [--include <prod|dev|optional|peer> [--include <prod|dev|optional|peer> ...]]
npm error [--strict-peer-deps] [--foreground-scripts] [--ignore-scripts] [--no-audit]
npm error [--no-bin-links] [--no-fund] [--dry-run]
npm error [-w|--workspace <workspace-name> [-w|--workspace <workspace-name> ...]]
npm error [--workspaces] [--include-workspace-root] [--install-links]
npm error
npm error aliases: clean-install, ic, install-clean, isntall-clean
npm error
npm error Run "npm help ci" for more info
npm error A complete log of this run can be found in: /Users/myuser/.npm/_logs/2025-03-25T23_59_08_151Z-debug-0.log

Additional information

0 verbose cli /Users/myuser/.nvm/versions/node/v20.18.3/bin/node /Users/myuser/.nvm/versions/node/v20.18.3/bin/npm
1 info using npm@11.2.0
2 info using node@v20.18.3
3 silly config load:file:/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/npmrc
4 silly config load:file:/Users/myuser/projects/work/pruned/json/.npmrc
5 silly config load:file:/Users/myuser/.npmrc
6 silly config load:file:/Users/myuser/.nvm/versions/node/v20.18.3/etc/npmrc
7 verbose title npm i
8 verbose argv "i"
9 verbose logfile logs-max:10 dir:/Users/myuser/.npm/_logs/2025-03-25T23_55_55_662Z-
10 verbose logfile /Users/myuser/.npm/_logs/2025-03-25T23_55_55_662Z-debug-0.log
11 silly logfile start cleaning logs, removing 1 files
12 silly packumentCache heap:4345298944 maxSize:1086324736 maxEntrySize:543162368
13 silly logfile done cleaning log files
14 verbose stack TypeError: Cannot read properties of undefined (reading 'extraneous')
14 verbose stack     at #loadLink (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/node_modules/@npmcli/arborist/lib/arborist/load-virtual.js:296:30)
14 verbose stack     at #resolveLinks (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/node_modules/@npmcli/arborist/lib/arborist/load-virtual.js:203:34)
14 verbose stack     at #loadFromShrinkwrap (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/node_modules/@npmcli/arborist/lib/arborist/load-virtual.js:91:29)
14 verbose stack     at Arborist.loadVirtual (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/node_modules/@npmcli/arborist/lib/arborist/load-virtual.js:63:35)
14 verbose stack     at async Arborist.buildIdealTree (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/node_modules/@npmcli/arborist/lib/arborist/build-ideal-tree.js:178:7)
14 verbose stack     at async Promise.all (index 1)
14 verbose stack     at async Arborist.reify (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/node_modules/@npmcli/arborist/lib/arborist/reify.js:131:5)
14 verbose stack     at async Install.exec (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/lib/commands/install.js:149:5)
14 verbose stack     at async Npm.exec (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/lib/npm.js:208:9)
14 verbose stack     at async module.exports (/Users/myuser/.nvm/versions/node/v20.18.3/lib/node_modules/npm/lib/cli/entry.js:67:5)
15 error Cannot read properties of undefined (reading 'extraneous')
16 silly unfinished npm timer reify 1742946955776
17 silly unfinished npm timer reify:loadTrees 1742946955777
18 silly unfinished npm timer idealTree:init 1742946955778
19 verbose cwd /projects/work/pruned/json
20 verbose os Darwin 24.3.0
21 verbose node v20.18.3
22 verbose npm  v11.2.0
23 verbose exit 1
24 verbose code 1
25 error A complete log of this run can be found in: /Users/myuser/.npm/_logs/2025-03-25T23_55_55_662Z-debug-0.log

package-lock.json has lockfileVersion set to 3.

And here is my Dockerfile snippet with relevant contents.

# Generate a partial monorepo with a pruned lockfile
# for a target workspace. The target workspace is
# the name specified in the workspace's package.json.
RUN turbo prune nectar-api --docker

# Add lockfile and package.json's of isolated sub-workspaces.
FROM base AS installer
RUN apk update && apk add --no-cache openssl
WORKDIR /app

ARG NPM_VERSION=${NPM_VERSION:-11.2.0}
RUN npm install --global npm@${NPM_VERSION}

# First, install the dependencies (including dev).
# This is done now because they change less often than the
# rest of the app's code.
COPY --from=builder /app/out/json/ .

# Note: running `npm install` also fails
RUN npm clean-install

# Second, copy the app source and build the project.
COPY --from=builder /app/out/full/ .```. 

[geemanjs]

Did you get anywhere / workaround this @dkindt? I've just run into the same issue.

[geemanjs]

After looking into this for a couple of hours, in my case there were a few issues.

1. I had a local package defined in my apps/web package.json which didn't exist in my repo anymore. I think npm install was passing as there was a copy in the apps/web package node_modules. npm install surprisingly raised no complaints
2. The crux of this issue was that the package-lock.json file contents doesn't match the package.json contents

I wonder if the turbo prune --docker command glosses over the issues (as ultimately they are package management ones) and this is where things get confusing.

Just in terms of getting to the bottom of this my method was:

1. Outside of docker reproduce the issue - for me this was simple as running turbo prune <my_app_name> --docker and then cd out/json and running npm ci
2. Once I was reproducing it I moved the package-lock.json file to package-lock-bak.json and then ran a clean npm install
3. At this point errors started popping out which I corrected in my project and went through steps 1/2 again.