Troubleshoot code quality workflows

Table of contents

This page covers common issues you might encounter when building code quality workflows with E2B sandboxes and MCP servers, along with their solutions.

If you're experiencing problems not covered here, check the E2B documentation.

MCP tools not available

Issue: Claude reports I don't have any MCP tools available.

Solution:

Verify you're using the authorization header:

--header "Authorization: Bearer ${mcpToken}"

Check you're waiting for MCP initialization:

await new Promise((resolve) => setTimeout(resolve, 1000));

await asyncio.sleep(1)

Ensure credentials are in both envs and mcp configuration:

const sbx = await Sandbox.betaCreate({
  envs: {
    ANTHROPIC_API_KEY: process.env.ANTHROPIC_API_KEY!,
    GITHUB_TOKEN: process.env.GITHUB_TOKEN!,
    SONARQUBE_TOKEN: process.env.SONARQUBE_TOKEN!,
  },
  mcp: {
    githubOfficial: {
      githubPersonalAccessToken: process.env.GITHUB_TOKEN!,
    },
    sonarqube: {
      org: process.env.SONARQUBE_ORG!,
      token: process.env.SONARQUBE_TOKEN!,
      url: "https://sonarcloud.io",
    },
  },
});

sbx = await AsyncSandbox.beta_create(
    envs={
        "ANTHROPIC_API_KEY": os.getenv("ANTHROPIC_API_KEY"),
        "GITHUB_TOKEN": os.getenv("GITHUB_TOKEN"),
        "SONARQUBE_TOKEN": os.getenv("SONARQUBE_TOKEN"),
    },
    mcp={
        "githubOfficial": {
            "githubPersonalAccessToken": os.getenv("GITHUB_TOKEN"),
        },
        "sonarqube": {
            "org": os.getenv("SONARQUBE_ORG"),
            "token": os.getenv("SONARQUBE_TOKEN"),
            "url": "https://sonarcloud.io",
        },
    },
)

Verify your API tokens are valid and have proper scopes.

GitHub tools work but SonarQube doesn't

Issue: GitHub MCP tools load but SonarQube tools don't appear.

Solution: SonarQube MCP server requires GitHub to be configured simultaneously. Always include both servers in your sandbox configuration, even if you're only testing one.

// Include both servers even if only using one
const sbx = await Sandbox.betaCreate({
  envs: {
    ANTHROPIC_API_KEY: process.env.ANTHROPIC_API_KEY!,
    GITHUB_TOKEN: process.env.GITHUB_TOKEN!,
    SONARQUBE_TOKEN: process.env.SONARQUBE_TOKEN!,
  },
  mcp: {
    githubOfficial: {
      githubPersonalAccessToken: process.env.GITHUB_TOKEN!,
    },
    sonarqube: {
      org: process.env.SONARQUBE_ORG!,
      token: process.env.SONARQUBE_TOKEN!,
      url: "https://sonarcloud.io",
    },
  },
});

# Include both servers even if only using one
sbx = await AsyncSandbox.beta_create(
    envs={
        "ANTHROPIC_API_KEY": os.getenv("ANTHROPIC_API_KEY"),
        "GITHUB_TOKEN": os.getenv("GITHUB_TOKEN"),
        "SONARQUBE_TOKEN": os.getenv("SONARQUBE_TOKEN"),
    },
    mcp={
        "githubOfficial": {
            "githubPersonalAccessToken": os.getenv("GITHUB_TOKEN"),
        },
        "sonarqube": {
            "org": os.getenv("SONARQUBE_ORG"),
            "token": os.getenv("SONARQUBE_TOKEN"),
            "url": "https://sonarcloud.io",
        },
    },
)

Claude can't access private repositories

Issue: "I don't have access to that repository".

Solution:

Verify your GitHub token has repo scope (not just public_repo).
Test with a public repository first.
Ensure the repository owner and name are correct in your .env:

GITHUB_OWNER=your_github_username
GITHUB_REPO=your_repository_name

GITHUB_OWNER=your_github_username
GITHUB_REPO=your_repository_name

Workflow times out or runs too long

Issue: Workflow doesn't complete or Claude credits run out.

Solutions:

Use timeoutMs: 0 (TypeScript) or timeout_ms=0 (Python) for complex workflows to allow unlimited time:

await sbx.commands.run(
  `echo '${prompt}' | claude -p --dangerously-skip-permissions`,
  {
    timeoutMs: 0, // No timeout
    onStdout: console.log,
    onStderr: console.log,
  },
);

await sbx.commands.run(
    f"echo '{prompt}' | claude -p --dangerously-skip-permissions",
    timeout_ms=0,  # No timeout
    on_stdout=print,
    on_stderr=print,
)

Break complex workflows into smaller, focused tasks.
Monitor your Anthropic API credit usage.
Add checkpoints in prompts: "After each step, show progress before continuing".

Sandbox cleanup errors

Issue: Sandboxes aren't being cleaned up properly, leading to resource exhaustion.

Solution: Always use proper error handling with cleanup in the finally block:

async function robustWorkflow() {
  let sbx: Sandbox | undefined;

  try {
    sbx = await Sandbox.betaCreate({
      // ... configuration
    });

    // ... workflow logic
  } catch (error) {
    console.error("Workflow failed:", error);
    process.exit(1);
  } finally {
    if (sbx) {
      console.log("Cleaning up sandbox...");
      await sbx.kill();
    }
  }
}

async def robust_workflow():
    sbx = None

    try:
        sbx = await AsyncSandbox.beta_create(
            # ... configuration
        )

        # ... workflow logic

    except Exception as error:
        print(f"Workflow failed: {error}")
        sys.exit(1)
    finally:
        if sbx:
            print("Cleaning up sandbox...")
            await sbx.kill()

Environment variable not loading

Issue: Script fails with "undefined" or "None" for environment variables.

Solution:

Ensure dotenv is loaded at the top of your file:

import "dotenv/config";

Verify the .env file is in the same directory as your script.
Check variable names match exactly (case-sensitive):

// .env file
GITHUB_TOKEN = ghp_xxxxx;

// In code
process.env.GITHUB_TOKEN; // Correct
process.env.github_token; // Wrong - case doesn't match

Ensure dotenv is loaded at the top of your file:

from dotenv import load_dotenv
load_dotenv()

Verify the .env file is in the same directory as your script.
Check variable names match exactly (case-sensitive):

# .env file
GITHUB_TOKEN=ghp_xxxxx

# In code
os.getenv("GITHUB_TOKEN")  # ✓ Correct
os.getenv("github_token")  # ✗ Wrong - case doesn't match

SonarQube returns empty results

Issue: SonarQube analysis returns no projects or issues.

Solution:

Verify your SonarCloud organization key is correct.
Ensure you have at least one project configured in SonarCloud.
Check that your SonarQube token has the necessary permissions.
Confirm your project has been analyzed at least once in SonarCloud.