CodeQL run for Java fails when PR has no changes in java files

[AndreyZendesk]

🏷️ Discussion Type

Bug

Body

Hi All,

I'm looking at the strange issue with CodeQL where it errors in "Finalizing java" step phase in PR that contain on markdown file changes. It's happened for one PR so far and I haven't seen any errors like this happening for other PRs in this and several other repos that use same workflow file.

I am trying to understand what's causing it but no luck so far.

This is the error:

Error: Encountered a fatal error while running "/opt/hostedtoolcache/CodeQL/2.25.1/x64/codeql/codeql database finalize --finalize-dataset --threads=4 --ram=14306 /home/runner/_work/_temp/codeql_databases/java". Exit code was 32 and last log line was: CodeQL detected code written in Java/Kotlin but this run didn't build any of it, or CodeQL could not process any of it. Ensure that you have provided manual build steps (see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages#about-specifying-build-steps-manually) for Java/Kotlin between the 'init' and 'analyze' Actions, and check the workflow run logs (see https://docs.github.com/en/actions/monitoring-and-troubleshooting-workflows/using-workflow-run-logs). For more information, review our troubleshooting guide at https://gh.io/troubleshooting-code-scanning/no-source-code-seen-during-build . See the logs for more details.

Screenshot:

Codeql workflow:

    strategy:
      fail-fast: false
      matrix:
        include:
          - language: java
            build-mode: manual
          - language: actions
            build-mode: none
            
    steps:
      - name: Checkout repository
        uses: actions/checkout@v5
        with:
          fetch-depth: 0

      - name: Initialize CodeQL
        uses: github/codeql-action/init@v4
        with:
          languages: ${{ matrix.language }}
          build-mode: ${{ matrix.build-mode }}

      - name: Set up JDK
        if: ${{ matrix.build-mode == 'manual' }}
        uses: actions/setup-java@v5.0.0
        with:
          distribution: 'zulu'
          java-version-file: .java-version
          cache: 'gradle'

      - name: Optimize Gradle properties for CI build
        if: ${{ matrix.build-mode == 'manual' }}
        run: |
          mkdir -p ~/.gradle
          cp gradle.properties ~/.gradle/gradle.properties

      - name: Build all modules
        if: ${{ matrix.build-mode == 'manual' }}
        run: ./gradlew assemble -x test --no-daemon

      - name: Perform CodeQL Analysis
        uses: github/codeql-action/analyze@v4
        with:
          category: "/language:${{matrix.language}}"

This screenshot shows successful build steps:

Files changed in PR:

Does anybody have an idea where to look for the hints or does it look like some weird edge case issue?

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