sqlite error: attempt to write a readonly database after 2.10.0 update

[wlipa (Bill Lipa)]

$ sudo port selfupdate
Password:
--->  Updating MacPorts base sources using rsync
MacPorts base version 2.9.3 installed,
MacPorts base version 2.10.0 downloaded.
--->  Updating the ports tree
--->  MacPorts base is outdated, installing new version 2.10.0
Installing new MacPorts release in /opt/local as root:wheel; permissions 0755


The ports tree has been updated. To upgrade your installed ports, you should run
  port upgrade outdated


$ port outdated
sqlite error: attempt to write a readonly database (8) while executing query: CREATE INDEX registry.snapshot_file_id ON snapshot_files(id)
    while executing
"registry::open $db_path"
    (procedure "mportinit" line 832)
    invoked from within
"mportinit ui_options global_options global_variations"
Error: /opt/local/bin/port: Failed to initialize MacPorts, sqlite error: attempt to write a readonly database (8) while executing query: CREATE INDEX registry.snapshot_file_id ON snapshot_files(id)

[jmroot (Joshua Root)]

It's attempting to update the registry database schema, but can't because it doesn't have write permissions. That theoretically should have already happened when the new version was being installed.

The workaround is easy at least: just run any port command with sudo, e.g. sudo port outdated.

[wlipa (Bill Lipa)]

Thank you, yes, that does work. However this error is not something I saw on previous versions.

[ryandesign (Ryan Carsten Schmidt)]

Not all new MacPorts base versions change the schema. Only those that do need write access to the database.

[jmroot (Joshua Root)]

That is true, but of course this is still a bug since the schema update should happen during make install. Any time mportinit is called should trigger it, and several scripts that do that are run at the end of installation, so I'm not sure how it didn't happen.

[ryandesign (Ryan Carsten Schmidt)]

Has duplicate #70523.

[bal-agates]

Sorry for the duplicate ticket. I did search but missed this one.

One other thing I noticed that could be related. The ​Change Log says:

- The number of outdated ports is printed after running
      'port selfupdate'. (#33820, thelastlin in 4ae6d98)

I did not see that. So maybe more than just the DB update is not getting executed?

[jmroot (Joshua Root)]

Replying to bal-agates:

One other thing I noticed that could be related. The ​Change Log says:

- The number of outdated ports is printed after running
      'port selfupdate'. (#33820, thelastlin in 4ae6d98)

I did not see that. So maybe more than just the DB update is not getting executed?

It will be printed only if the number is not zero, so there's probably nothing to worry about unless you did have some outdated ports. Oh, and also the selfupdate that installed the new version was run by the old version, so it would not have this feature. You would only see it with future selfupdates.

[wlipa (Bill Lipa)]

Is there a log for what happened during the self update? Or a verbose mode... I have some other computers to upgrade.

[ryandesign (Ryan Carsten Schmidt)]

selfupdate does not save a log. If you run selfupdate on the command line you can run it with the -d flag to generate debug output and you can redirect that output to a file if you want. If you use the installer package, you can choose Installer Log from the Window menu and in that window change the Detail Level from Show Errors Only to Show All Logs. You can click the Save button in that window if you want to save it to a file.

[bal-agates]

When I did the selfupdate upgrading to 2.10.0 I had outdated ports but nothing on stdout indicating the count outdated. Here is the entire selfupdate output:

$ sudo port selfupdate
Password:
--->  Updating MacPorts base sources using rsync
MacPorts base version 2.9.3 installed,
MacPorts base version 2.10.0 downloaded.
--->  Updating the ports tree
--->  MacPorts base is outdated, installing new version 2.10.0
Installing new MacPorts release in /opt/local as root:wheel; permissions 0755


The ports tree has been updated. To upgrade your installed ports, you should run
  port upgrade outdated

I used "sudo port outdated" to workaround the DB schema update. This showed 356 ports that were outdated.

Now when I run "sudo port selfupdate" I do see the message counting outdated ports:

$ sudo port selfupdate
Password:
--->  Checking for newer releases of MacPorts
MacPorts base version 2.10.0 installed,
MacPorts base version 2.10.0 available.
--->  MacPorts base is already the latest version
--->  Updating the ports tree

The ports tree has been updated.

356 ports are outdated. Run 'port outdated' for details.
To upgrade your installed ports, you should run
  port upgrade outdated

So the code to report the outdated count was not run on my selfupdate from 2.9.3 to 2.10.0. Was that selfupdate output from the 2.9.3 exe? Could that also explain why the DB schema was not updated?

[jmroot (Joshua Root)]

Replying to bal-agates:

So the code to report the outdated count was not run on my selfupdate from 2.9.3 to 2.10.0. Was that selfupdate output from the 2.9.3 exe?

Yes, as I said in my edit to comment:7.

Could that also explain why the DB schema was not updated?

No, or this would have happened for every previous version that changed the database schema, which is quite a lot of them.

[gctwnl]

After doing a first portindex that fails like this, I did a second one with sudo. After that, the one without sudo works. And ownership of the Portindex and Portindex.quick files are still normal user me. Weird.

(I am using an alternate sources location)

[jmroot (Joshua Root)]

Looking at the registry of an installation that just selfupdated to 2.10.0, the version field is 1.214. It becomes 1.215 when fully updated, and it was 1.211 for MacPorts 2.9.3, which means most of the schema updates happened correctly, just not the last one. Still no idea why.

[programmingkidx]

Just wanted to note I saw this problem when I ran 'sudo port selfupdate'. The installed version was 2.9.3 and the downloaded version was 2.10.1. This was on Mac OS 10.5.

[programmingkidx]

Forgot to mention that the solution to this issue for me was to download the installer and run it.

[jmroot (Joshua Root)]

I'm sure that worked, but there are much easier ways. See comment:1.

[mascguy (Christopher Nielsen)]

Just upgraded from 2.9.3 to 2.10.1 today, and now I'm seeing this error constantly when trace mode is enabled. Here are just two examples, but it's consistent across ports.

Note: Normally I enable verbose mode too, as the goal is to validate dependencies, expected behavior, etc. But it's not used for these examples, to reduce the noise.

Example 1, for gtk3:

$ sudo port -t configure gtk3 +quartz
--->  Computing dependencies for gtk3
--->  Fetching distfiles for gtk3
sqlite error: attempt to write a readonly database (8)
--->  Verifying checksums for gtk3
sqlite error: attempt to write a readonly database (8)
--->  Extracting gtk3
Warning: The following existing file was hidden from the build system by trace mode:
  /private/var/select/sh
Warning: The following file inside the MacPorts prefix not installed by a port was accessed:
  /opt/local/etc/gitconfig
sqlite error: attempt to write a readonly database (8)
--->  Applying patches to gtk3
Warning: The following existing file was hidden from the build system by trace mode:
  /private/var/select/sh
--->  Configuring gtk3
sqlite error: attempt to write a readonly database (8)

Example 2, for fop2:

$ sudo port -t configure fop2
--->  Fetching distfiles for fop2
sqlite error: attempt to write a readonly database (8)
--->  Verifying checksums for fop2
sqlite error: attempt to write a readonly database (8)
--->  Extracting fop2
Warning: The following existing file was hidden from the build system by trace mode:
  /private/var/select/sh
sqlite error: attempt to write a readonly database (8)
sqlite error: attempt to write a readonly database (8)
--->  Configuring fop2
sqlite error: attempt to write a readonly database (8)

Is this expected behavior for 2.10.x...?