Git GPG Error: database_open Waiting for Lock

Problem Statement

When attempting Git operations that require GPG signing (such as commits), you may encounter a blocking error where GPG appears stuck indefinitely. The error typically shows:

gpg: Note: database_open 134217901 waiting for lock (held by 9857) ...
[GNUPG:] FAILURE sign 134250628
gpg: signing failed: Operation timed out

Or repeatedly displays:

--list-keys
gpg: Note: database_open 134217901 waiting for lock (held by 9857) ...
gpg: Note: database_open 134217901 waiting for lock (held by 9857) ...

Key Symptoms

• Git operations hang during signing verification
• GPG reports waiting for a lock held by a process ID (PID)
• Commit/push operations fail after timeout periods
• Issue persists after token resets, repository clones, or credential updates
• Commonly observed in RStudio and terminal Git operations

Solution: Remove GPG Lock File

The core issue is a conflicting lock file in GPG's directory. This commonly occurs when a previous GPG process crashed or failed to release resources properly.

Default GPG Path

Solutions assume GPG's home directory is at ~/.gnupg. If you have a custom GNUPGHOME environment variable, adjust paths accordingly.

Step-by-Step Fix

1. Terminate existing GPG processes:

   gpgconf --kill all

2. Remove the lock file causing the conflict:

   rm -f ~/.gnupg/S.gpg-agent

3. Verify resolution by listing GPG keys:

   gpg --list-keys

   Successful execution confirms the lock is released.

Alternate Approach for Persistent Locks

If the error persists, remove all GPG lock files (use cautiously):

rm -f ~/.gnupg/*.lock

Workaround: Temporarily Disable GPG Signing

If your workflow doesn't require signed commits, temporarily disable signing to bypass the issue.

Disable per Repository

# Disable signing for current repo
git config commit.gpgsign false

Disable Globally

# Disable signing for all repositories
git config --global commit.gpgsign false

WARNING

This bypasses security verification. Re-enable signing once the lock issue is resolved:

git config commit.gpgsign true

Why This Works

Root Cause Analysis

• GPG uses lock files to prevent concurrent access to sensitive operations
• When a Git signing process crashes (e.g., due to timeout or system interrupt), it leaves a stale lock
• Subsequent operations hang indefinitely waiting for the orphaned lock

Solution Benefits Over Disabling Signing

• Maintains commit verification integrity
• Addresses the underlying file system conflict
• Prevents recurrence in future signing operations
• Doesn't compromise security workflows

Additional Troubleshooting

If issues persist:

1. Identify locking process:

   ps aux | grep 9857  # Replace 9857 with PID from error

2. Kill the process if it's orphaned:

   kill -9 9857

3. Refresh GPG connections:

   gpg-connect-agent reloadagent /bye

---

Reference Solution: Git Commit Freeze Fix