How do I fix a vulnerable npm package in my package-lock.json that isn't listed in the package.json?

Question

It sounds like Hoek is a dependency of one of your dependencies (so, a package you have in your package.json is requiring it from it's own package.json).

You've already tried deleting/reinstalling and updating your project dependencies without success, so it seems that the package dependency in question has an explicit or max version specified.

Without seeing the package.json for each of your dependencies, it would be difficult to advise further on how to force an update.

Edit: To help you identify which packages are using which dependencies, you can use NPM's ls command: https://docs.npmjs.com/cli/ls

For example, to see which packages are using Hoek: npm ls hoek

Edit 2: As Ulysse BN correctly points out, if you have NPM version 6 or later, you can use npm audit fix to ask NPM to attempt to fix the vulnerabilities for you.

Edit 3: Those reading this should also check out JBallin's answer below. It expands on information I have given here, and is (in my opinion) a more structured answer that addresses OP's question better. However - if you want a quick fix - this answer should suffice.

TLDR: Update the parent package using npm i $PARENT_PKG_NAME.

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Note

When updating dependencies, you should review the CHANGELOG for any breaking changes.

Diagnosis

npm audit will reveal both the vulnerable package (note that you'll need a package-lock.json file for this, so you'll need to run npm i), as well as the package that it is a dependency of (if applicable). Note that you can also use npm ls $CHILD_PKG_NAME to see its parent dependencies.

Quick Fix Attempt

npm audit fix and npm audit fix --force are worth a try, but sometimes the fix will need to be done manually (see below).

Manual Fix

Most likely the parent package will have already fixed their dependencies (you can verify this by going to their GitHub and reviewing the recent commits--or just seeing if this fixes it), so you can just run npm i $PARENT_PKG_NAME @$NEW_VERSION and it will update your package-lock.json.

If parent has not fixed the vulnerability

If the maintainer doesn't seem to be responsive, you may consider using an alternative package that accomplishes the same thing or forking the package and updating the vulnerability yourself.

Verify Fix

You can now verify that it worked by running npm audit and ensuring that no vulnerabilities are showing up. Commit your changes, push them to GitHub, refresh your notifications/alerts and they should be gone!

If you have npm@6 or later, you can use npm audit fix for your security issues.

Edit package-lock.json manually and update vulnerable package version to the fixed one and then use

npm ci

That will install the packages according to package-lock.json by ignoring package.json first. Then use

npm audit fix

again, to be sure if it's properly done. If it does not help so, then use other given solutions.

More Information here:

https://blog.npmjs.org/post/171556855892/introducing-npm-ci-for-faster-more-reliable

or here: https://docs.npmjs.com/auditing-package-dependencies-for-security-vulnerabilities

Use:

npm i hoek

npm will install the latest version of hoek and your package.lock.json become updated.

To check vulnerable npm packages, just use following commands:

npm audit

To fix vulnerable npm packages, just use following commands which will fix package-lock.json too:

npm audit fix