WARN: Could not find ref 'refs/heads/develop' in refs/heads, refs/remotes, refs/remotes/upstream or

SonarQube Server / Community Build
1
  • Developer Edition v2025.1 (102418), MQR Mode
  • SonarQube deployed: Docker
  • I am trying to create incremental scaning

Dear SonarQube Support,

I am encountering an issue during pull request analysis using dotnet-sonarscanner in a TeamCity CI environment.

:red_exclamation_mark: Problem Summary

We receive the following warning in the Sonar logs:

WARN: Could not find ref 'refs/heads/develop' in refs/heads, refs/remotes, refs/remotes/upstream or refs/remotes/origin

As a result:

  • :white_check_mark: Cache is working
Downloading cache. Project key: Test2.BE, branch: refs/heads/develop.
Incremental PR analysis: 12041 files out of 12104 are unchanged.
Pre-processing succeeded.
  • :cross_mark: Changed files are not detected
  • :white_check_mark: Incremental PR analysis is working

:hammer_and_wrench: Context

My script is here:

#!/bin/bash
set -o xtrace -o pipefail -o errexit -o nounset

SONAR_PROJECT_KEY=Test2.BE
SONAR_TOKEN=*******
SONAR_URL=http://some_url.net:9000/
SONAR_QGATE_WAIT=true
TEAMCITY_BUILD_BRANCH=merge-requests/5231
TEAMCITY_TARGET_BRANCH_SHORT=develop
TEAMCITY_SOURCE_BRANCH_SHORT=Sonar-test

TARGET_BRANCH_REF="refs/heads/$TEAMCITY_TARGET_BRANCH_SHORT"
SOURCE_BRANCH_REF="refs/heads/$TEAMCITY_SOURCE_BRANCH_SHORT"

echo "Using branch name: $TEAMCITY_BUILD_BRANCH"
echo "Target branch ref: $TARGET_BRANCH_REF"
echo "Source branch ref: $SOURCE_BRANCH_REF"

apt update
apt-get install --yes openjdk-17-jre
dotnet tool install --global dotnet-sonarscanner
dotnet tool install --global dotnet-coverage

# === Git config & fix for shared reference clones ===
git config --global --add safe.directory '*'
git remote set-url origin "https://oauth2:${GITLAB_TOKEN}@gitlab.test.com/as/oo/test2.be.git"

echo "=== Cleaning up possible Git reference issues ==="
if [ -f .git/objects/info/alternates ]; then
    echo "⚠️  Detected alternates file in .git — removing to avoid shared object issues..."
    cat .git/objects/info/alternates
    rm .git/objects/info/alternates
else
    echo "✅ No alternates file detected — OK"
fi

# === Fetch full refs from origin ===
git fetch --unshallow || echo "Not a shallow clone"
git fetch origin "+refs/heads/*:refs/remotes/origin/*"

# Ensure local target branch exists and is checked out
echo "Ensuring local branch for $TEAMCITY_TARGET_BRANCH_SHORT exists and checked out"
git fetch origin "$TEAMCITY_TARGET_BRANCH_SHORT"

MERGE_BASE=$(git merge-base HEAD origin/$TEAMCITY_TARGET_BRANCH_SHORT)
    
echo "MERGE_BASE: $MERGE_BASE"

# === Sonar analysis ===
if [[ $TEAMCITY_BUILD_BRANCH == merge-requests/* ]]; then
    PULL_REQUEST_ID=$(echo $TEAMCITY_BUILD_BRANCH | cut -d'/' -f2)

    echo "Running Sonar analysis for merge request"
    echo "MR IID: $PULL_REQUEST_ID"
    echo "MR SOURCE BRANCH: $SOURCE_BRANCH_REF"
    echo "MR TARGET BRANCH: $TARGET_BRANCH_REF"

    /root/.dotnet/tools/dotnet-sonarscanner begin \
        /k:$SONAR_PROJECT_KEY \
        /d:sonar.host.url=$SONAR_URL \
        /d:sonar.token=$SONAR_TOKEN \
        /d:sonar.qualitygate.wait=$SONAR_QGATE_WAIT \
        /d:sonar.pullrequest.key="$PULL_REQUEST_ID" \
        /d:sonar.pullrequest.branch="$TEAMCITY_SOURCE_BRANCH_SHORT" \
        /d:sonar.pullrequest.base="$TARGET_BRANCH_REF" \
        /d:sonar.pullrequest.provider="gitlab" \
        /d:sonar.scm.revision="$MERGE_BASE" \
        /d:sonar.scm.provider=git \
        /d:sonar.cs.vscoveragexml.reportsPaths=coverage.xml \
        /d:sonar.scanner.scanAll=false
else
    echo "Running Sonar analysis for branch"
    /root/.dotnet/tools/dotnet-sonarscanner begin \
        /k:$SONAR_PROJECT_KEY \
        /d:sonar.host.url=$SONAR_URL \
        /d:sonar.token=$SONAR_TOKEN \
        /d:sonar.qualitygate.wait=$SONAR_QGATE_WAIT \
        /d:sonar.branch.name="$TEAMCITY_BUILD_BRANCH" \
        /d:sonar.cs.vscoveragexml.reportsPaths=coverage.xml \
        /d:sonar.scanner.scanAll=false
fi

dotnet build ./Test2.BE.sln
/root/.dotnet/tools/dotnet-coverage collect "dotnet test Test2.BE.sln --filter Category!=IntegrationTests" -f xml -o "coverage.xml"
/root/.dotnet/tools/dotnet-sonarscanner end /d:sonar.token=$SONAR_TOKEN

When I am using the values TARGET_BRANCH_REF and SOURCE_BRANCH_REF w/o “refs/heads/…” I have the next result:

  • :cross_mark: Cache doesn’t work and error about refs/heads/develop not appeared anymore
  • :white_check_mark: Changed files are detected
  • :cross_mark: Incremental PR analysis fails, it started to check all files

:man_raising_hand: Our Question

What is the wrong here, or recommended approach to ensure that the base branch (e.g., refs/heads/develop) is available locally so that SonarQube can correctly analyze the diff?

  • Can SonarQube work with refs/remotes/origin/develop directly?
  • Is there a supported way to avoid this checkout issue, or bypass the local refs/heads/* requirement?

We would appreciate any guidance you can provide.

2

Hi,

Welcome to the community!

That “Could not find” message is about the SCM metadata available to analysis. You’ll need to make sure the prerequisites are in place.

 
HTH,
Ann