nix-collect-garbage: error getting outputs of ... database disk image is malformed

[ambrop72]

I started getting these errors and I can no longer collect garbage.

# nix-collect-garbage 
finding garbage collector roots...
deleting garbage...
deleting '...'
...
deleting '...'
error: error getting outputs of ‘/nix/store/3zhh42kb125zmxi9kfqn6c6xxbzvggi2-gtk2-engines.deb.drv’: database disk image is malformed
0 store paths deleted, 0.00 MiB freed

The error is not always for the same file. Attached are 3 example drv files for which the error occurs.
errors.zip

[ambrop72]

I ran nix-store --verify --check-contents --repair and it succeeded without finding any issue.

[edolstra]

Can you try

sqlite3 /nix/var/nix/db/db.sqlite 'pragma integrity_check'

This should print ok.

[ambrop72]

Hi,
I actually already worked around this issue (by deleting the GC root that was pulling in the problematic drvs and manually deleting these drvs, don't know if the latter was necessary). So while I don't know what this test would have done before I did that, now it does say ok.

[sjmackenzie]

> sqlite3 /nix/var/nix/db/db.sqlite 'pragma integrity_check' 
*** in database main ***
Page 957: btreeInitPage() returns error code 11
Page 13391: btreeInitPage() returns error code 11
Page 6178: btreeInitPage() returns error code 11
Page 10204: btreeInitPage() returns error code 11
Page 7794: btreeInitPage() returns error code 11
Error: database disk image is malformed

[clacke]

I'll try the solution the original reporter used -- track down the derivations responsible and evict them.

[clacke]

It wasn't possible. This fixed the issue:

# cd /nix/var/nix/db
# nix-shell -p sqlite

[nix-shell:/nix/var/nix/db]# sqlite3 db.sqlite ".backup 'db.bak.sqlite' "

[nix-shell:/nix/var/nix/db]# sqlite3 db.sqlite 
SQLite version 3.24.0 2018-06-04 19:24:41
Enter ".help" for usage hints.
sqlite> .output db.sql
sqlite> .dump
sqlite> 

[nix-shell:/nix/var/nix/db]# sqlite3 db.new.sqlite < db.sql

[nix-shell:/nix/var/nix/db]# mv db.new.sqlite db.sqlite

I was hoping that simply using the backup would be good enough, but it retained the corruption. It was necessary to make a textual export and rebuild the database.

[573]

It wasn't possible. This fixed the issue:

# nix-shell -p sqlite

[nix-shell:/nix/var/nix/db]# sqlite3 db.sqlite ".backup 'db.bak.sqlite' "

[nix-shell:/nix/var/nix/db]# sqlite3 db.sqlite 
SQLite version 3.24.0 2018-06-04 19:24:41
Enter ".help" for usage hints.
sqlite> .output db.sql
sqlite> .dump
sqlite> 

[nix-shell:/nix/var/nix/db]# sqlite3 db.new.sqlite < db.sql

[nix-shell:/nix/var/nix/db]# mv db.new.sqlite db.sqlite

I was hoping that simply using the backup would be good enough, but it retained the corruption. It was necessary to make a textual export and rebuild the database.

At first I forgot the cd /nix/var/nix/db step before running that but that fixed it indeed.

[clacke]

Oh yes! Sorry for not being explicit. Edited my previous comment to include the cd step.

[ghuntley]

This issue could be closed. I also experienced corruption but that was related to running out of disk space on /nix (future folx, make sure you check this!)

[stale]

I marked this as stale due to inactivity. → More info