GitHub Actions update with PR closed by dependabot for different version update ignored due to "Pull request already exists for actions/setup-node with latest version 4"

### Is there an existing issue for this?

- [X] I have searched the existing issues

### Package ecosystem

Github actions

### Package manager version

_No response_

### Language version

_No response_

### Manifest location and content before the Dependabot update

In one file:
```
- name: Set up Node.js
uses: actions/setup-node@v2
with:
node-version-file: ./docs/.nvmrc
```

In another:

```
- uses: actions/setup-node@v4
with:
node-version-file: ./website/.nvmrc
```

### dependabot.yml content

```
version: 2
updates:
- package-ecosystem: github-actions
directory: /
schedule:
interval: weekly

...

```

### Updated dependency

_No response_

### What you expected to see, versus what you actually saw

Dependabot should update `actions/setup-node` from 2 to 4

Related to https://github.com/dependabot/dependabot-core/issues/7214 which is closed as "completed". However here the problem seems slightly different, with an existing PR wrongly parsed by dependabot.

This issue appears somewhat similar to https://github.com/dependabot/dependabot-core/issues/7543 as well

### Native package manager behavior

No PR is opened to update the action at v2 to v4.

### Images of the diff or a link to the PR, issue, or logs

Logs from dependabot show that somehow dependabot thinks a PR already exists:

```
updater | 2024/05/06 18:40:21 INFO Checking if actions/setup-node 2 needs updating
proxy | 2024/05/06 18:40:21 [170] GET https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:21 [170] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [170] 200 https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 4
updater | 2024/05/06 18:40:21 INFO Pull request already exists for actions/setup-node with latest version 4
updater | 2024/05/06 18:40:21 INFO Checking if actions/checkout 4 needs updating
```

Full logs:

```
proxy | 2024/05/06 18:40:00 proxy starting, commit: d85fbd08cee81b78b7f408b09b558cac7a0cee5c
proxy | 2024/05/06 18:40:00 Listening (:1080)
updater | 2024-05-06T18:40:01.239986175 [824564858:main:WARN:src/devices/src/legacy/serial.rs:222] Detached the serial input due to peer close/error.
updater | time="2024-05-06T18:40:03Z" level=info msg="guest starting" commit=7ae3c8b6b9717f8ad3c56d9958b08ec3c5b6c903
updater | time="2024-05-06T18:40:03Z" level=info msg="starting job..." fetcher_timeout=10m0s job_id=824564858 updater_timeout=45m0s updater_version=687fcdbc1775f2acef290b4513e864df52cb95b1-github-actions
updater | /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/httparty-0.21.0/lib/httparty.rb:10: warning: csv was loaded from the standard library, but will no longer be part of the default gems since Ruby 3.4.0. Add csv to your Gemfile or gemspec. Also contact author of httparty-0.21.0 to add csv into its gemspec.
updater | 2024/05/06 18:40:07 INFO Starting job processing
updater | 2024/05/06 18:40:07 INFO Job definition: {"job":{"allowed-updates":[{"dependency-type":"direct","update-type":"all"}],"commit-message-options":{"include-scope":null,"prefix":null,"prefix-development":null},"credentials-metadata":[{"host":"github.com","type":"git_source"}],"debug":null,"dependencies":null,"dependency-group-to-refresh":null,"dependency-groups":[],"existing-group-pull-requests":[],"existing-pull-requests":[[{"dependency-name":"actions/setup-node","dependency-version":"4"}],[{"dependency-name":"actions/upload-artifact","dependency-version":"3"}]],"experiments":{"proxy-cached":true,"record-ecosystem-versions":true,"record-update-job-unknown-error":true},"ignore-conditions":[],"lockfile-only":false,"max-updater-run-time":2700,"package-manager":"github_actions","proxy-log-response-body-on-auth-failure":true,"reject-external-code":false,"repo-private":true,"requirements-update-strategy":null,"security-advisories":[],"security-updates-only":false,"source":{"api-endpoint":"https://api.github.com/","branch":null,"directory":"/.","hostname":"github.com","provider":"github","repo":"loculus-project/loculus"},"update-subdependencies":false,"updating-a-pull-request":false,"vendor-dependencies":false}}
updater |
proxy | 2024/05/06 18:40:07 [002] GET https://github.com:443/loculus-project/loculus/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:07 [002] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:07 [002] 200 https://github.com:443/loculus-project/loculus/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:07 [004] POST https://github.com:443/loculus-project/loculus/git-upload-pack
proxy | 2024/05/06 18:40:07 [004] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:07 [004] 200 https://github.com:443/loculus-project/loculus/git-upload-pack
proxy | 2024/05/06 18:40:07 [006] POST https://github.com:443/loculus-project/loculus/git-upload-pack
proxy | 2024/05/06 18:40:07 [006] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:08 [006] 200 https://github.com:443/loculus-project/loculus/git-upload-pack
updater | 2024/05/06 18:40:08 INFO Base commit SHA: c0bd326763a8f701acc5c34c1303e01ed27c710a
updater | 2024/05/06 18:40:08 INFO Finished job processing
updater | time="2024-05-06T18:40:08Z" level=info msg="task complete" container_id=job-824564858-file-fetcher exit_code=0 job_id=824564858 step=fetcher
updater | /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/httparty-0.21.0/lib/httparty.rb:10: warning: csv was loaded from the standard library, but will no longer be part of the default gems since Ruby 3.4.0. Add csv to your Gemfile or gemspec. Also contact author of httparty-0.21.0 to add csv into its gemspec.
updater | 2024/05/06 18:40:11 INFO Starting job processing
proxy | 2024/05/06 18:40:12 [008] GET https://github.com:443/fergusmacd/github-action-usage.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [008] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:12 [008] 200 https://github.com:443/fergusmacd/github-action-usage.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [010] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [010] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:12 [010] 200 https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [012] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [012] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:12 [012] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [014] GET https://github.com:443/actions/setup-java.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [014] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:12 [014] 200 https://github.com:443/actions/setup-java.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [016] GET https://github.com:443/gradle/actions.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [016] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:12 [016] 200 https://github.com:443/gradle/actions.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [018] GET https://github.com:443/nick-fields/retry.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [018] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:12 [018] 200 https://github.com:443/nick-fields/retry.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [020] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [020] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:12 [020] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [022] GET https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:12 [022] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [022] 200 https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [024] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [024] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [024] 200 https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [026] GET https://github.com:443/actions/setup-java.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [026] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [026] 200 https://github.com:443/actions/setup-java.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [028] GET https://github.com:443/gradle/actions.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [028] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [028] 200 https://github.com:443/gradle/actions.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [030] GET https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [030] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [030] 200 https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [032] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [032] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [032] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [034] GET https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [034] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [034] 200 https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [036] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [036] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [036] 200 https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [038] GET https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:13 [038] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:13 [038] 200 https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [040] GET https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [040] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [040] 200 https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [042] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [042] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [042] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [044] GET https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [044] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [044] 200 https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [046] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [046] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [046] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [048] GET https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [048] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [048] 200 https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [050] GET https://github.com:443/peaceiris/actions-gh-pages.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [050] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [050] 200 https://github.com:443/peaceiris/actions-gh-pages.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [052] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [052] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [052] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [054] GET https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [054] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [054] 200 https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [056] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:14 [056] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:14 [056] 200 https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [058] GET https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [058] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:15 [058] 200 https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [060] GET https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [060] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:15 [060] 200 https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [062] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [062] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:15 [062] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [064] GET https://github.com:443/azure/setup-helm.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [064] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:15 [064] 200 https://github.com:443/azure/setup-helm.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [066] GET https://github.com:443/wyrihaximus/github-action-helm3.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [066] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:15 [066] 200 https://github.com:443/wyrihaximus/github-action-helm3.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [068] GET https://github.com:443/actions/upload-artifact.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [068] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:15 [068] 200 https://github.com:443/actions/upload-artifact.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [070] GET https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [070] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:15 [070] 200 https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [072] GET https://github.com:443/actions/cache.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [072] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:15 [072] 200 https://github.com:443/actions/cache.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [074] GET https://github.com:443/lewagon/wait-on-check-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:15 [074] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [074] 200 https://github.com:443/lewagon/wait-on-check-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [076] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [076] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [076] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [078] GET https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [078] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [078] 200 https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [080] GET https://github.com:443/actions/cache.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [080] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [080] 200 https://github.com:443/actions/cache.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [082] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [082] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [082] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [084] GET https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [084] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [084] 200 https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [086] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [086] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [086] 200 https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [088] GET https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [088] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [088] 200 https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [090] GET https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [090] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:16 [090] 200 https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:16 [092] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
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proxy | 2024/05/06 18:40:17 [094] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
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proxy | 2024/05/06 18:40:17 [096] GET https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [096] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:17 [096] 200 https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [098] GET https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [098] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:17 [098] 200 https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [100] GET https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
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proxy | 2024/05/06 18:40:17 [100] 200 https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [102] GET https://github.com:443/azure/setup-helm.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [102] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:17 [102] 200 https://github.com:443/azure/setup-helm.git/info/refs?service=git-upload-pack
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proxy | 2024/05/06 18:40:17 [104] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [106] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [106] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:17 [106] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [108] GET https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:17 [108] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:17 [108] 200 https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [110] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [110] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:18 [110] 200 https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [112] GET https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [112] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:18 [112] 200 https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [114] GET https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [114] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:18 [114] 200 https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [116] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [116] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:18 [116] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [118] GET https://github.com:443/lewagon/wait-on-check-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [118] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:18 [118] 200 https://github.com:443/lewagon/wait-on-check-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [120] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [120] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:18 [120] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [122] GET https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [122] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:18 [122] 200 https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [124] GET https://github.com:443/actions/cache.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [124] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:18 [124] 200 https://github.com:443/actions/cache.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [126] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:18 [126] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:19 [126] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [128] GET https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [128] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:19 [128] 200 https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [130] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [130] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:19 [130] 200 https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [132] GET https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [132] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:19 [132] 200 https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [134] GET https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [134] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:19 [134] 200 https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:19 INFO Starting update job for loculus-project/loculus
updater | 2024/05/06 18:40:19 INFO Checking all dependencies for version updates...
updater | 2024/05/06 18:40:19 INFO Checking if peaceiris/actions-gh-pages 4 needs updating
proxy | 2024/05/06 18:40:19 [140] GET https://github.com:443/peaceiris/actions-gh-pages.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:19 [140] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:19 [140] 200 https://github.com:443/peaceiris/actions-gh-pages.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:20 INFO Latest version is 4
updater | 2024/05/06 18:40:20 INFO No update needed for peaceiris/actions-gh-pages 4
updater | 2024/05/06 18:40:20 INFO Checking if fergusmacd/github-action-usage 0.9.2 needs updating
proxy | 2024/05/06 18:40:20 [144] GET https://github.com:443/fergusmacd/github-action-usage.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:20 [144] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:20 [144] 200 https://github.com:443/fergusmacd/github-action-usage.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:20 INFO Latest version is 0.9.2
updater | 2024/05/06 18:40:20 INFO No update needed for fergusmacd/github-action-usage 0.9.2
updater | 2024/05/06 18:40:20 INFO Checking if nick-fields/retry 3 needs updating
proxy | 2024/05/06 18:40:20 [146] GET https://github.com:443/nick-fields/retry.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:20 [146] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:20 [146] 200 https://github.com:443/nick-fields/retry.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:20 INFO Latest version is 3
updater | 2024/05/06 18:40:20 INFO No update needed for nick-fields/retry 3
updater | 2024/05/06 18:40:20 INFO Checking if docker/setup-buildx-action 3 needs updating
proxy | 2024/05/06 18:40:20 [148] GET https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:20 [148] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:20 [148] 200 https://github.com:443/docker/setup-buildx-action.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:20 INFO Latest version is 3
updater | 2024/05/06 18:40:20 INFO No update needed for docker/setup-buildx-action 3
updater | 2024/05/06 18:40:20 INFO Checking if WyriHaximus/github-action-helm3 4 needs updating
proxy | 2024/05/06 18:40:20 [150] GET https://github.com:443/wyrihaximus/github-action-helm3.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:20 [150] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:20 [150] 200 https://github.com:443/wyrihaximus/github-action-helm3.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:20 INFO Latest version is 4
updater | 2024/05/06 18:40:20 INFO No update needed for WyriHaximus/github-action-helm3 4
updater | 2024/05/06 18:40:20 INFO Checking if actions/setup-java 4 needs updating
proxy | 2024/05/06 18:40:20 [152] GET https://github.com:443/actions/setup-java.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:20 [152] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:20 [152] 200 https://github.com:443/actions/setup-java.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:20 INFO Latest version is 4
updater | 2024/05/06 18:40:20 INFO No update needed for actions/setup-java 4
updater | 2024/05/06 18:40:20 INFO Checking if docker/metadata-action 5 needs updating
proxy | 2024/05/06 18:40:20 [154] GET https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:20 [154] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:20 [154] 200 https://github.com:443/docker/metadata-action.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:20 INFO Latest version is 5
updater | 2024/05/06 18:40:20 INFO No update needed for docker/metadata-action 5
updater | 2024/05/06 18:40:20 INFO Checking if docker/build-push-action 5 needs updating
proxy | 2024/05/06 18:40:20 [156] GET https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:20 [156] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:20 [156] 200 https://github.com:443/docker/build-push-action.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:20 INFO Latest version is 5
updater | 2024/05/06 18:40:20 INFO No update needed for docker/build-push-action 5
updater | 2024/05/06 18:40:20 INFO Checking if actions/upload-artifact 4 needs updating
proxy | 2024/05/06 18:40:20 [158] GET https://github.com:443/actions/upload-artifact.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:20 [158] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [158] 200 https://github.com:443/actions/upload-artifact.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 4
updater | 2024/05/06 18:40:21 INFO No update needed for actions/upload-artifact 4
updater | 2024/05/06 18:40:21 INFO Checking if docker/login-action 3 needs updating
proxy | 2024/05/06 18:40:21 [160] GET https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:21 [160] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [160] 200 https://github.com:443/docker/login-action.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 3
updater | 2024/05/06 18:40:21 INFO No update needed for docker/login-action 3
updater | 2024/05/06 18:40:21 INFO Checking if azure/setup-helm 4 needs updating
proxy | 2024/05/06 18:40:21 [162] GET https://github.com:443/azure/setup-helm.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:21 [162] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [162] 200 https://github.com:443/azure/setup-helm.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 4
updater | 2024/05/06 18:40:21 INFO No update needed for azure/setup-helm 4
updater | 2024/05/06 18:40:21 INFO Checking if actions/cache 4 needs updating
proxy | 2024/05/06 18:40:21 [164] GET https://github.com:443/actions/cache.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:21 [164] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [164] 200 https://github.com:443/actions/cache.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 4
updater | 2024/05/06 18:40:21 INFO No update needed for actions/cache 4
updater | 2024/05/06 18:40:21 INFO Checking if lewagon/wait-on-check-action 1.3.4 needs updating
proxy | 2024/05/06 18:40:21 [166] GET https://github.com:443/lewagon/wait-on-check-action.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:21 [166] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [166] 200 https://github.com:443/lewagon/wait-on-check-action.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 1.3.4
updater | 2024/05/06 18:40:21 INFO No update needed for lewagon/wait-on-check-action 1.3.4
updater | 2024/05/06 18:40:21 INFO Checking if gradle/actions 3 needs updating
proxy | 2024/05/06 18:40:21 [168] GET https://github.com:443/gradle/actions.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:21 [168] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [168] 200 https://github.com:443/gradle/actions.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 3
updater | 2024/05/06 18:40:21 INFO No update needed for gradle/actions 3
updater | 2024/05/06 18:40:21 INFO Checking if actions/setup-node 2 needs updating
proxy | 2024/05/06 18:40:21 [170] GET https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:21 [170] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [170] 200 https://github.com:443/actions/setup-node.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 4
updater | 2024/05/06 18:40:21 INFO Pull request already exists for actions/setup-node with latest version 4
updater | 2024/05/06 18:40:21 INFO Checking if actions/checkout 4 needs updating
proxy | 2024/05/06 18:40:21 [172] GET https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
proxy | 2024/05/06 18:40:21 [172] * authenticating git server request (host: github.com)
proxy | 2024/05/06 18:40:21 [172] 200 https://github.com:443/actions/checkout.git/info/refs?service=git-upload-pack
updater | 2024/05/06 18:40:21 INFO Latest version is 4
updater | 2024/05/06 18:40:21 INFO No update needed for actions/checkout 4
updater | 2024/05/06 18:40:21 INFO Finished job processing
updater | time="2024-05-06T18:40:22Z" level=info msg="task complete" container_id=job-824564858-updater exit_code=0 job_id=824564858 step=updater
```

Now it turns out there are 2 PRs (one merged one closed) but they are for different files and different updates (from 3 -> 4) and dependabot closed them itself.

The one that's closed was closed by dependabot itself

So this looks very clearly like a real bug. Though a bit tricky to reproduce. I'll update by hand now.

### Smallest manifest that reproduces the issue

_No response_

Reproduce the update using the two workflow files containing actions/setup-node@v2 and @v4, plus the shown dependabot.yml configuration. Start by tracing how the github_actions updater interprets existing-pull-requests in the logs; done means the v2 reference is recognized independently and a PR to update it to v4 can be opened.

Written by the indexing model from the issue text.