NationalSecurityAgency/ghidra · error · SQLException

failed to delete H2-file database: {}

Error message

failed to delete H2-file database: {}

What it means

Thrown as an SQLException by H2FileFunctionDatabase.dropDatabase() when fileDs.delete() returns false after the database has been verified as a valid BSim database and the data source has been disposed. The H2 file data source was unable to delete the underlying database files from disk.

Source

Thrown at Ghidra/Features/BSim/src/main/java/ghidra/features/bsim/query/file/H2FileFunctionDatabase.java:159

			try (ResultSet rs = st.executeQuery(
				"SELECT table_name FROM information_schema.tables WHERE table_schema = 'public' ORDER BY table_name")) {
				while (rs.next()) {
					tableNames.add(rs.getString(1));
				}
			}
		}

		// Spot check for a few BSim table names that always exist
		if (!tableNames.contains("keyvaluetable") || !tableNames.contains("desctable") ||
			!tableNames.contains("weighttable")) {
			throw new SQLException("attempted to drop non-BSim database");
		}

		fileDs.dispose(); // disconnect before deleting database

		BSimServerInfo serverInfo = fileDs.getServerInfo();
		if (!fileDs.delete()) {
			throw new SQLException("failed to delete H2-file database: " + serverInfo);
		}

		Msg.info(this, "Deleted BSim H2-file database: " + serverInfo);

	}

	/**
	 * Create vector map which maps vector ID to {@link VectorStoreEntry}
	 * @return vector map
	 * @throws SQLException if error occurs while reading map data
	 */
	public Map<Long, VectorStoreEntry> readVectorMap() throws SQLException {
		return vectorTable.readVectors();
	}

	@Override
	protected int deleteVectors(long id, int countdiff) throws SQLException {
		return vectorTable.deleteVector(id, countdiff);

View on GitHub (pinned to d5f144c24d)

Solutions

1. Check for processes holding the file open (lsof on Linux, Resource Monitor on Windows) and close them.
2. Verify file system write/delete permissions on the database directory.
3. Remove any stale H2 lock files (.lock.db, .lock.db.trace.db) manually after ensuring no process is active.
4. Retry the drop after a brief delay if a transient OS lock (backup/AV scan) is the cause.
5. As a last resort, shut down all processes and manually delete the database files from the OS.

Example fix

// before
db.dropDatabase(); // delete() returns false

// after
try {
    db.dropDatabase();
} catch (SQLException e) {
    if (e.getMessage().contains("failed to delete")) {
        // clear stale locks and retry
        Files.deleteIfExists(dbPath.resolve("bsim.lock.db"));
        Thread.sleep(1000);
        Files.deleteIfExists(dbPath);
    } else throw e;
}

// Check file writability/deletability before drop
if (!Files.isWritable(dbPath)) {
    throw new IllegalStateException(
        "Database file is not writable/deletable: " + dbPath);
}
// Check no external process holds the file (Linux)
// (platform-specific; on Linux use lsof, on Windows use Resource Monitor)

try {
    database.dropDatabase();
} catch (SQLException e) {
    if (e.getMessage().startsWith("failed to delete H2-file database:")) {
        // Clear locks and retry with OS-level deletion
        Path lockFile = dbPath.resolveSibling(dbPath.getFileName() + ".lock.db");
        Files.deleteIfExists(lockFile);
        Files.deleteIfExists(dbPath);
    } else {
        throw e;
    }
}

When it happens

Trigger: Occurs when the BSim tables are confirmed present, fileDs.dispose() succeeds (disconnecting the pool), but fileDs.delete() returns false. This happens due to: OS-level file locking by another process, insufficient file system permissions, read-only file system, or the file being held open by an external process (antivirus, backup, IDE).

Common situations: Antivirus or backup software is scanning the database file. Another process (different JVM, file manager) has the file open. Running on a read-only or permission-restricted file system. The H2 lock file wasn't properly cleaned up. Network-mounted file system with delayed lock release.

Related errors

• database in use
• attempted to drop non-BSim database
• Missing databaseName for drop database
• Could not create database:
• Database does not exist: {}

AI-assisted analysis of NationalSecurityAgency/ghidra@d5f144c24d (2026-08-14). Data as JSON: /api/errors/b8b033f2c0a2b05b. Report an issue: GitHub.