Unable to upgrade from 2025-09 in Desktop2 MacOS
roger.gordon@ithinking.co.uk
I have Databases (0) from the Local instances tab. Running on MacOS. Version Version 2.1.1 (2.1.1). Databases created with 2025-09. I made a separate post of the Database list issue.
NB: the Data directory is on an external drive, but I think this is a Desktop2 issue since neo4j-admin will back up all DBs and I can connect to all 3 of them (system, default neo4j and one more for testing)
When I try to upgrade I get a message that the Data folder must exist (it has been redirected in neo4j.conf to an external file using server.directories.data=....)
roger.gordon@ithinking.co.uk
Hi all, ended up doing a complete reinstall and restoring the database. The restore of the database backup fails unless Desktop 2 is shutdown and restarted several times, but eventually got there. YMMV - make sure you have good backups!
Nissanka Fernando
Hi Roger,
Have you set the Desktop custom data path? Take a look here:
roger.gordon@ithinking.co.uk
Nissanka Fernando - disaster!
I followed instructions and a second desktop keeps popping up. Neo4j confused about where database files are. Now Neo4j not starting.
I have a full backup from before I tried the plist. There should be NO transactions pending btw....
I deleted the plist file after a launchctl unload and then a restart. no joy:
2025-12-30 11:48:19.396+0000 INFO ======== Neo4j 2025.09.0 ========
2025-12-30 11:48:19.428+0000 INFO This instance is ServerId{e30d7f67} (e30d7f67-a3f1-4f2a-96d7-b9efa8baf8fd)
2025-12-30 11:48:19.569+0000 INFO Resolved endpoints with LIST{endpoints:'[localhost:6000]'} to '[localhost:6000]'
2025-12-30 11:48:19.592+0000 INFO Resolved endpoints with LIST{endpoints:'[localhost:6000]'} to '[localhost:6000]'
2025-12-30 11:48:31.787+0000 ERROR Failed to start Neo4j on localhost:7474.
java.lang.RuntimeException: Error starting Neo4j database server at /Volumes/T7/neo4j/data/databases
...
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'com.neo4j.dbms.reconciler.operators.SystemOperator@31f295b6' was successfully initialized, but failed to start. Please see the attached cause exception "Fail to start 'DatabaseId{00000000[system]}' since transaction logs were found, while database files are missing.".
roger.gordon@ithinking.co.uk
Just looked in the external drive and Neo4j Desktop has
wiped
out the entire database. Nissanka Fernando any thoughts?Nissanka Fernando
Hello roger.gordon@ithinking.co.uk! I have a few more questions for you:
- Can you provide more details about the error message you receive when attempting to upgrade?
- Have you tried any troubleshooting steps, such as moving the Data directory back to the local drive, to see if the issue persists?
- Is there any specific reason for redirecting the Data directory to an external drive, and have you encountered similar issues with other versions?
roger.gordon@ithinking.co.uk
Nissanka Fernando thanks for your response...
There's that weird 0 Databases issue - don't know if that's relevant or just a quirky thing.
- The database is over 400gb so won't fit on my HD. Thats possibly an issue for the normal upgrade since it want to put a backup in
/Users/rogergordon/Library/Application%20Support/neo4j-desktop/Application/Data/backups
- same issue as 3 above, but do note that I have changed the original data directory under the install to data-old-- to be clearer this is on the hard drive -- the external drive is as expected: /data/....
- will run this again but the logs showed that it wanted the data directory (perhaps for the backup).
Is the neo4j.conf file read for the upgrade? The server.directories.dumps.root property is directed to and external drive and not the Application Support directory....
roger.gordon@ithinking.co.uk
Nissanka Fernando, the backup is successful (only about 80gb), but then Desktop flashes onto a create your first instance screen.
The log entry in the upgrade-logs folder has an empty neo4j.log file and the relate.debug.json shows:
{"os":"darwin","backup":"/Users/rogergordon/Library/Application Support/neo4j-desktop/Application/Data/backups/backup-ed192354-3194-4dfc-9bdf-c148ba37dd5c","sourceDbms":{"id":"c4a02801-2701-41c2-86d1-41a350923a00","version":"2025.09.0","path":"/Users/rogergordon/Library/Application Support/neo4j-desktop/Application/Data/dbmss/dbms-c4a02801-2701-41c2-86d1-41a350923a00","plugins":["apoc"]},"targetDbms":{"id":"51b1fe8e-b32c-434b-952d-495ea0699df1","version":"2025.11.2","path":"/Users/rogergordon/Library/Application Support/neo4j-desktop/Application/Data/dbmss/dbms-51b1fe8e-b32c-434b-952d-495ea0699df1"}}