When updating groups where at least one package is lockfile-only, re-runs lose all package.json updates

[anomiex]

How are you running Renovate?

Self-hosted Renovate

If you're self-hosting Renovate, tell us which platform (GitHub, GitLab, etc) and which version of Renovate.

GitHub

Please tell us more about your question or problem

If you have a group of packages configured, and at least one package in the group needs a package.json update while at least one other package in the group needs a lockfile-only update, Renovate re-runs will frequently lose all package.json updates from the PR.

More specifically: On the first run it creates the PR for the group normally. On the second run it finds no package.json updates are needed (because the PR already contains them) but still sees that there's a package with a lockfile-only update, so it redoes the PR with only the lockfile update (throwing away the package.json changes). A third re-run will redo the package.json updates.

Minimal reproduction repo: https://github.com/anomiex/renovate-test/

Logs (if relevant)

Logs

https://github.com/anomiex/renovate-test/actions/runs/12126600506

DEBUG: packageFiles with updates (repository=anomiex/renovate-test, baseBranch=master)
       "config": {
         "github-actions": [
           {
             "deps": [
               {
                 "depName": "actions/checkout",
                 "commitMessageTopic": "{{{depName}}} action",
                 "datasource": "github-tags",
                 "versioning": "docker",
                 "depType": "action",
                 "replaceString": "actions/checkout@v4",
                 "autoReplaceStringTemplate": "{{depName}}@{{#if newDigest}}{{newDigest}}{{#if newValue}} # {{newValue}}{{/if}}{{/if}}{{#unless newDigest}}{{newValue}}{{/unless}}",
                 "currentValue": "v4",
                 "updates": [],
                 "packageName": "actions/checkout",
                 "warnings": [],
                 "sourceUrl": "https://github.com/actions/checkout",
                 "registryUrl": "https://github.com",
                 "currentVersion": "v4",
                 "currentVersionTimestamp": "2024-10-23T14:24:28.000Z",
                 "currentVersionAgeInDays": 40,
                 "fixedVersion": "v4"
               },
               {
                 "depName": "renovatebot/github-action",
                 "commitMessageTopic": "{{{depName}}} action",
                 "datasource": "github-tags",
                 "versioning": "docker",
                 "depType": "action",
                 "replaceString": "renovatebot/github-action@v41.0.5",
                 "autoReplaceStringTemplate": "{{depName}}@{{#if newDigest}}{{newDigest}}{{#if newValue}} # {{newValue}}{{/if}}{{/if}}{{#unless newDigest}}{{newValue}}{{/unless}}",
                 "currentValue": "v41.0.5",
                 "updates": [],
                 "packageName": "renovatebot/github-action",
                 "warnings": [],
                 "sourceUrl": "https://github.com/renovatebot/github-action",
                 "registryUrl": "https://github.com",
                 "currentVersion": "v41.0.5",
                 "currentVersionTimestamp": "2024-11-29T21:09:21.000Z",
                 "currentVersionAgeInDays": 2,
                 "fixedVersion": "v41.0.5"
               },
               {
                 "depName": "ubuntu",
                 "currentValue": "latest",
                 "replaceString": "ubuntu-latest",
                 "depType": "github-runner",
                 "datasource": "github-runners",
                 "autoReplaceStringTemplate": "{{depName}}-{{newValue}}",
                 "skipReason": "invalid-version",
                 "updates": [],
                 "packageName": "ubuntu"
               }
             ],
             "packageFile": ".github/workflows/renovate.yml"
           }
         ],
         "npm": [
           {
             "deps": [
               {
                 "depType": "dependencies",
                 "depName": "noop6",
                 "currentValue": "^1.0.0",
                 "datasource": "npm",
                 "prettyDepType": "dependency",
                 "lockedVersion": "1.0.0",
                 "updates": [
                   {
                     "bucket": "non-major",
                     "newVersion": "1.0.9",
                     "newValue": "^1.0.0",
                     "releaseTimestamp": "2020-08-09T14:31:55.691Z",
                     "newVersionAgeInDays": 1576,
                     "newMajor": 1,
                     "newMinor": 0,
                     "newPatch": 9,
                     "updateType": "patch",
                     "isRange": true,
                     "isLockfileUpdate": true,
                     "branchName": "renovate-sh/group"
                   }
                 ],
                 "packageName": "noop6",
                 "versioning": "npm",
                 "warnings": [],
                 "sourceUrl": "https://github.com/IonicaBizau/noop6",
                 "registryUrl": "https://registry.npmjs.org",
                 "currentVersion": "1.0.0",
                 "currentVersionTimestamp": "2016-03-02T10:46:18.843Z",
                 "currentVersionAgeInDays": 3197,
                 "isSingleVersion": true,
                 "fixedVersion": "1.0.0"
               },
               {
                 "depType": "dependencies",
                 "depName": "chalk",
                 "currentValue": "4.0.0",
                 "datasource": "npm",
                 "prettyDepType": "dependency",
                 "lockedVersion": "4.0.0",
                 "updates": [
                   {
                     "bucket": "non-major",
                     "newVersion": "4.1.2",
                     "newValue": "4.1.2",
                     "releaseTimestamp": "2021-07-30T12:02:52.839Z",
                     "newVersionAgeInDays": 1221,
                     "newMajor": 4,
                     "newMinor": 1,
                     "newPatch": 2,
                     "updateType": "minor",
                     "branchName": "renovate-sh/group"
                   },
                   {
                     "bucket": "major",
                     "newVersion": "5.3.0",
                     "newValue": "5.3.0",
                     "releaseTimestamp": "2023-06-29T10:58:11.887Z",
                     "newVersionAgeInDays": 522,
                     "newMajor": 5,
                     "newMinor": 3,
                     "newPatch": 0,
                     "updateType": "major",
                     "branchName": "renovate-sh/major-group"
                   }
                 ],
                 "packageName": "chalk",
                 "versioning": "npm",
                 "warnings": [],
                 "sourceUrl": "https://github.com/chalk/chalk",
                 "registryUrl": "https://registry.npmjs.org",
                 "currentVersion": "4.0.0",
                 "currentVersionTimestamp": "2020-04-02T08:20:33.785Z",
                 "currentVersionAgeInDays": 1705,
                 "isSingleVersion": true,
                 "fixedVersion": "4.0.0"
               },
               {
                 "depType": "engines",
                 "depName": "pnpm",
                 "currentValue": "^9.0.0",
                 "datasource": "npm",
                 "commitMessageTopic": "pnpm",
                 "prettyDepType": "engine",
                 "updates": [],
                 "packageName": "pnpm",
                 "versioning": "npm",
                 "warnings": [],
                 "sourceUrl": "https://github.com/pnpm/pnpm",
                 "registryUrl": "https://registry.npmjs.org",
                 "sourceDirectory": "pnpm",
                 "homepage": "https://pnpm.io",
                 "currentVersion": "9.14.4",
                 "currentVersionTimestamp": "2024-11-29T10:56:56.250Z",
                 "currentVersionAgeInDays": 3
               }
             ],
             "extractedConstraints": {"pnpm": "^9.0.0"},
             "managerData": {
               "hasPackageManager": false,
               "pnpmShrinkwrap": "pnpm-lock.yaml",
               "yarnZeroInstall": false
             },
             "skipInstalls": true,
             "packageFile": "package.json",
             "lockFiles": ["pnpm-lock.yaml"]
           }
         ]
       }

DEBUG: syncBranchState() (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: syncBranchState(): Branch cache not found, creating minimal branchState (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: getBranchPr(renovate-sh/group) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: findPr(renovate-sh/group, undefined, open) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Found PR #29 (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: branchExists=true (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: dependencyDashboardCheck=undefined (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: PR rebase requested=false (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Checking if PR has been edited (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: branch.isModified(): using git to calculate (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: branch.isModified() = false (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Found existing branch PR (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Checking schedule(schedule=at any time, tz=null, now=2024-12-02T19:32:53.604Z) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: No schedule defined (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: GET https://api.github.com/repos/anomiex/renovate-test/branches/master/protection = (code=ERR_NON_2XX_3XX_RESPONSE, statusCode=404 retryCount=0, duration=104) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: No branch protection found for master (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Converting rebaseWhen=auto to rebaseWhen=conflicted because no rule for behind-base-branch applies (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Branch already exists (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Skipping behind base branch check due to rebaseWhen=conflicted (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: isBranchConflicted(master, renovate-sh/group) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: branch.isConflicted(): using git to calculate (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Setting git author name: Renovate Bot (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Setting git author email: bot@renovateapp.com (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: branch.isConflicted(): false (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Branch does not need rebasing (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Using reuseExistingBranch: true (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Setting current branch to master (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: latest commit (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "branchName": "master",
       "latestCommitDate": "2024-12-02T14:24:20-05:00"
DEBUG: manager.getUpdatedPackageFiles() reuseExistingBranch=true (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: npm.updateDependency(): dependencies.chalk = 4.1.2 (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Cannot patch pnpm lock file directly - falling back to using pnpm (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: updateArtifacts for nonUpdatedPackageFiles (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: npm.updateArtifacts(package.json) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: No packageManager updates - returning null (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: No package files need updating (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Getting updated lock files (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Writing package.json files (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "packageFiles": ["package.json"]
DEBUG: Writing any updated package files (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Found 0 npm host rule(s) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Writing updated .npmrc file to .npmrc (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Generating pnpm-lock.yaml for . (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Spawning pnpm install to create pnpm-lock.yaml (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Found pnpm constraint in package.json engines: ^9.0.0 (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: No node constraint found - using latest (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Performing lockfileUpdate (pnpm) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Setting CONTAINERBASE_CACHE_DIR to /tmp/renovate/cache/containerbase (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Using containerbase dynamic installs (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Using queue: host=nodejs.org, concurrency=16 (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Resolved stable matching version (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "toolName": "node",
       "constraint": null,
       "resolvedVersion": "v22.11.0"
DEBUG: Resolved stable matching version (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "toolName": "pnpm",
       "constraint": "^9.0.0",
       "resolvedVersion": "9.14.4"
DEBUG: Executing command (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "command": "install-tool node v22.11.0"
DEBUG: exec completed (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "durationMs": 4210,
       "stdout": "[19:32:54.405] INFO (372): Installing tool node@22.11.0...\nv22.11.0\n10.9.0\n0.29.4\n[19:32:57.747] INFO (372): Install tool node succeeded in 3.3s.\n",
       "stderr": ""
DEBUG: Executing command (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "command": "install-tool pnpm 9.14.4"
DEBUG: exec completed (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "durationMs": 2200,
       "stdout": "[19:32:58.614] INFO (409): Installing npm pnpm@9.14.4...\n9.14.4\n[19:33:00.311] INFO (409): Install tool pnpm succeeded in 1.7s.\n",
       "stderr": ""
DEBUG: Executing command (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "command": "pnpm install --recursive --lockfile-only --ignore-scripts --ignore-pnpmfile"
DEBUG: exec completed (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "durationMs": 454,
       "stdout": "Done in 418ms\n",
       "stderr": ""
DEBUG: Executing command (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "command": "pnpm update --no-save noop6@1.0.9 --recursive --lockfile-only --ignore-scripts --ignore-pnpmfile"
DEBUG: exec completed (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "durationMs": 999,
       "stdout": "Progress: resolved 1, reused 0, downloaded 0, added 0\nProgress: resolved 7, reused 0, downloaded 0, added 0, done\nDone in 964ms\n",
       "stderr": ""
DEBUG: Executing command (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "command": "pnpm dedupe --config.ignore-scripts=true"
DEBUG: exec completed (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "durationMs": 781,
       "stdout": "Progress: resolved 1, reused 0, downloaded 0, added 0\nAlready up to date\nProgress: resolved 7, reused 0, downloaded 7, added 7, done\n\ndependencies:\n+ chalk 4.0.0 (5.3.0 is available)\n+ noop6 1.0.9\n\n",
       "stderr": ""
DEBUG: pnpm-lock.yaml needs updating (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Updated 1 lock files (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "updatedArtifacts": ["pnpm-lock.yaml"]
DEBUG: Getting comments for #29 (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: http cache: saving https://api.github.com/repos/anomiex/renovate-test/issues/29/comments?per_page=100 (etag="43b24f4ee81a7434c0f690bc20457c912de0e686d8fec0bf74a9ae2e8afd5d12", lastModified=undefined) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Found 0 comments (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Getting comments for #29 (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: http cache: saving https://api.github.com/repos/anomiex/renovate-test/issues/29/comments?per_page=100 (etag="43b24f4ee81a7434c0f690bc20457c912de0e686d8fec0bf74a9ae2e8afd5d12", lastModified=undefined) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Found 0 comments (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: 1 file(s) to commit (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Preparing files for committing to branch renovate-sh/group (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: git commit (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "deletedFiles": [],
       "ignoredFiles": [],
       "result": {
         "author": null,
         "branch": "renovate-sh/group",
         "commit": "7f5ee782362664fddf42cd4047bac27d5b7ba5c6",
         "root": false,
         "summary": {"changes": 1, "insertions": 4, "deletions": 4}
       }
DEBUG: Pushing refSpec renovate-sh/group:renovate-sh/group (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: git push (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "result": {
         "pushed": [],
         "ref": {"local": "refs/remotes/origin/renovate-sh/group"},
         "remoteMessages": {"all": []}
       }
DEBUG: Setting current branch to master (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: latest commit (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "branchName": "master",
       "latestCommitDate": "2024-12-02T14:24:20-05:00"
 INFO: Branch updated (repository=anomiex/renovate-test, branch=renovate-sh/group)
       "commitSha": "7f5ee782362664fddf42cd4047bac27d5b7ba5c6"
DEBUG: Ensuring PR (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: There are 0 errors and 0 warnings (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: getBranchPr(renovate-sh/group) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: findPr(renovate-sh/group, undefined, open) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Found PR #29 (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Found existing PR (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Fetching changelog: https://github.com/chalk/chalk (4.0.0 -> 4.1.2) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Fetching changelog: https://github.com/IonicaBizau/noop6 (1.0.0 -> 1.0.9) (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Processing existing PR (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: setPrCache() (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: Pull Request #29 does not need updating (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: PR is not configured for automerge (repository=anomiex/renovate-test, branch=renovate-sh/group)
DEBUG: setBranchCommit() (repository=anomiex/renovate-test, branch=renovate-sh/group)

[github-actions[bot]]

Hi there,

Get your discussion fixed faster by creating a minimal reproduction. This means a repository dedicated to reproducing this issue with the minimal dependencies and config possible.

Before we start working on your issue we need to know exactly what's causing the current behavior. A minimal reproduction helps us with this. Discussions without reproductions are less likely to be converted to Issues.

Please follow these steps:

1. Read our guide on creating a minimal reproduction.
2. Go to our minimal reproduction template repository.
3. Select the Use this template button to create a new repository based on the template.
4. Work on the minimal reproduction in your own repository.
5. Fill out the information in your repository's README.md.
6. Add the link to your reproduction to the first post of your Discussion. If you are not the original author, you can post a new comment with the link.

If you need help with running renovate on your minimal reproduction repository, please refer to our Running Renovate guide.
Good luck,

The Renovate team

[rarkins]

Please see our automated guide to reproductions. Your repo is missing a description, also has some unnecessary complexity

[anomiex]

Removing the config.js makes the self-hosted Renovate fail to run correctly, but I removed it for you anyway. 🤷

[rarkins]

Now install the hosted app, and try to reproduce the problem you described

[anomiex]

Do you no longer support self-hosted?

[rarkins]

It's important to isolate if this is related to your environment or other settings, or also reproduces in the hosted app

[anomiex]

Isn't isolating it what the minimal reproduction repo is for? You can see exactly what it runs and with what configuration there, since it even uses your GitHub Action to do the self-hosting.

I was respectful of your time in taking my time to reduce it to a minimal self-hosted example. But I don't have more time to spend on this right now to chase it into your hosted environment.

[github-actions[bot]]

Hi there,

We're closing this discussion because it's missing some details, or because something else about it made it hard or impossible for us to help resolve the issue.

We want high quality discussions, so users can search them for answers. This means we'll close (and later delete) low quality discussions.

You are welcome to create a new discussion with more details in future.

Thanks, the Renovate team.