Dependency Graph shows outdated versions and 13 stale Dependabot alerts

[slx-slx]

🏷️ Discussion Type

Bug

💬 Feature/Topic Area

Dependabot

Discussion Details

Bug: Dependency Graph reports outdated npm versions

Repository: https://github.com/slx-slx/s2-verification
Current main commit: 3bbc42e

Our repository continues to show 13 Dependabot alerts
(2 critical, 5 high, 5 moderate, 1 low), although all
affected dependencies were updated on October 27, 2026.

GitHub Dependency Graph vs. current package-lock.json:

• next: GitHub 16.3.6 / Current 16.4.2
• sharp: GitHub 0.35.4 / Current 0.35.5
• source-map-js: GitHub 1.2.1 / Current 1.2.2
• zod: GitHub 4.6.5 / Current 4.6.7

Both npm audit and npm audit --omit=dev report
zero vulnerabilities.

Steps to reproduce:

1. Open the repository's Dependency Graph.
2. Observe outdated versions attributed to package-lock.json.
3. Compare them with the current package-lock.json on main.
4. Manually refresh Dependabot alerts.

Actual result:
The outdated versions and all 13 alerts remain visible.

Expected result:
The Dependency Graph should recognize the patched versions
and reconcile alerts for dependencies no longer present.

There is only one root npm lockfile and no GitHub Actions
dependency-submission workflow.

Could the GitHub team investigate this discrepancy?
We prefer not to dismiss the alerts manually.

[github-actions[bot]]

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[RooTinfinite]

The Dependency Graph did not update the database because either the GitHub-side indexing webhook hung, or the parser encountered a silent error in the structure of package-lock.json and retained the previous state of the repository.
Until the internal dependency graph processes the new commit, Dependabot will not automatically close the alerts, even though npm audit returns zero vulnerabilities locally.

How to fix this immediately without manually clicking on the alerts:

In the repository, go to Settings → Code security and analysis.

Disable the Dependency graph option, then re-enable it after one minute—this will force a full reindex of the main branch.

Alternatively, make an empty commit that affects the manifest (git commit --allow-empty -m “trigger graph” && git push) to generate a new push event for the GitHub parser.